With the history that Trump had for firing people who did follow unreasonable orders (e.g. Rod Rosenstein), it becomes entirely plausible that he would fire any FDA head who did not support a vaccine, regardless of the science behind them. As things turned out, the studies did support the vaccine, but it was not unreasonable to draw a distinction between unbiased experts and experts under threat of firing.

The vaccines didn't exist at that point; We didn't know how effective or safe they would turn out to be (at least in their first iteration), so obviously it would have been ridiculous to commit blindly to taking them.

Once trial results were released, we learned that they're highly effective and that risks of bad reactions are exceedingly rare (especially when compared to the effects of the virus itself).