If a player is willing to lower their spell resistance to someone casting a spell on them, what choices do they have open to them?
If they have spellcraft they have the ability to tell what spell is being cast, but at what point, and could they resume their SR fast enough to try and be protected?
Would the SR be down regardless of what they were trying to do?
So, unless the casting time of the spell goes beyond the start of the creature's next turn, its spell resistance stays down while the spell is being cast.
This answer by @ShadowKras shows that by readying its standard action to drop SR when it detects a benign spell being cast, a creature can reduce its risk. Its SR is then down until that initiative count on the following round, however. So it's a trade-off, though since SR isn't easily detectable, it's generally moderately safe to do.