> Because their licence gave Facebook the upper hand if they wanted to come after you.
No it didn't. Facebook made a nothing-up-the-sleeve showing; you had recourse if they decided to "come after you", because your right to countersue was something that was explicitly protected in the PATENTS grant.
Removing the grant, on the other hand, contributes to a world where everyone else can come after you. That should be scarier, because the set containing entities who aren't Facebook is much larger than the set of entities who are. (And the latter set is much less likely to sue—virtually guaranteed not to sue, even—for the exact reason mentioned above.)