Was the Tower perhaps the only card that originally bore an image that caused discomfort to early tarot players in the 15th century?
First, let's make it clear that nothing else seems to have made them particularly uncomfortable. They don't seem to have been unduly disturbed by either Death or the Devil, or by the Traitor. The religious figures in the deck (including the angels and the pope) gave great offense to many pious people, as we know from the Steele Sermon and from the various attempts (successful or unsuccessful) to eliminate those figures from tarot decks in the 15th, 16th, and 17th centuries. But there's no indication that those who actually played tarot were ever offended by those religious figures, and in any case being offended is not the same as feeling uncomfortable or perturbed: even the author of the Steele Sermon might have felt only outrage, never disquiet.
But the Tower might have been different.
Its earliest known name is the Thunderbolt, and it was probably originally intended to represent God smiting evil with lightning, thus triumphing over the Devil and his works (and thus forming a useful bridge in the trump order: the Thunderbolt beats the Devil but is inferior to the greater celestial light of the Star).
But the card's designer seems to have chosen to represent that with a fairly conventional type of "Tower of Babel" image, showing people falling down towards a devil at the base of the tower—and that devil probably didn't look terribly discomfited.
This reconstruction of the original design is based on a comparison of all the surviving historical cards, which finds that four elements are very likely to have been present on the original card:
- A fortified tower, with crenellations at the top
- Lightning striking it, probably causing visible damage to it
- Human figures (probably two, maybe just one) falling from the tower
- A devil at the base of the tower, maybe depicted only with its head visible, emerging from behind the tower or from its doorway
I'm assuming that all four of these were present originally because:
- They (or likely descendants of them) all appear in different design lineages from different regions
- The first two seem essential because they are present in some form on nearly all cards
- The latter two are present less frequently, but must surely be original because it is hard to imagine that they would have been added in multiple different regions if they were not there to begin with.
The original image probably looked a little like the mid-15th century Tower of Babel that Mike drew our attention to in 2010.

Villabianca in the 18th century appears to have called the old Sicilian Tower card il novissimo dell'anima = "the last judgment of the soul" (Dummett, Il Mondo e l'Angelo p. 299; Dummett and McLeod, A History of Games Played With the Tarot Deck vol. 1 p. 373 note 3). Given that the sight of that Sicilian card inspired much the same tristezza (melancholy, suffering, unpleasantness) as the Sicilian Devil card did at that time, we can fairly safely assume that it depicted only a soul or souls being damned to hell, and not any souls being raised to heaven. Since this disquieting design was then replaced by a simple tower, it's very probable that the card Villabianca was describing clearly depicted at least three of the elements listed above: the tower, the human figure(s) (although possibly not shown falling) and a devil. It probably showed the lightning in some form too, interpreted as signifying divine judgment.
There were probably a lot of people who similarly saw the Tower card as depicting the damnation of souls, even in the earliest years, regardless of the designer's intention.
The Sicilian deck seems to have been the only one anywhere that preserved the original design elements intact to such an extent as late as the 18th century. The Roman tarot deck almost certainly had a very similar Tower, because the Sicilian deck seems to have been a direct and close descendant of the Roman one, and a Roman name for the card was casa del dan[n]ato (house of the damned). But the Roman deck seems to have died out by Villabianca's time.
In all other regions, at least one of the vital elements was removed much earlier: the Charles VI deck and the Rosenwald deck (both probably descended from a common source) removed both the devil and the human figures already in the 15th century; the Venetian version did the same, either in the 15th or early 16th century. The Bolognese one removed the devil, probably also before the end of the 15th century. On the evidence of the Cary sheet and the Tarot de Marseille, it seems the Milanese deck did that too, and likewise in the 15th century, but in that case a remnant of the devil seems to have stayed for a while in the form of a cow (the early tarot devils nearly always had cow's ears and horns, so this transformation is not too surprising). The Vieville version (which I suspect came from Piedmont but it could have been from another Lombard lineage) took that Milanese development a lot further, turning the cow into a small flock, the exploding tower into a tree, and the human figure into a shepherd. The Minchiate version, probably an offshoot from the same Central Italian lineage that produced the Roman and Sicilian cards, likewise retained nearly all the original elements, but the person (only one now) was no longer falling and the image no longer clearly implied damnation. We don't know what the Ferrarese card looked like but it must have kept the devil like Minchiate did, because the Bertoni poem calls the card Casa del Diavolo and Lollio and Imperiali call it Inferno, but Il Sivello describes it as an infiammata casa, so it could have just shown a flaming building with a devil in it, with nothing obviously indicating the damnation of souls in that version either.
Were all these changes merely the result of the usual process of playing-card design evolution, with people being confused about what they were seeing and/or trying to embellish the design in small ways? Yet all of the changes effectively moved the design in the same direction, namely away from the suggestion of damnation. So maybe a lot of people in the 15th century and possibly the early 16th century disliked that aspect so much that they felt an urge to remove it from the image.
Why should that have made the players so very uncomfortable? Well, the reason might have been all those preachers like San Bernardino, Savonarola and the author of the Steele Sermon, constantly banging on about how people who played cards would go to hell. That might have preyed on players' minds just a little too much for them to feel happy being constantly reminded of it by the image presented to them on this card.