Yes, we require the caster to beat the SR if the spell in question has a Spell Resistance: yes entry, regardless if the spell is benificial or harmfull, cast by friends or enemies etc.
During our last big battle the party cleric cast Mass Spell Resistance on everyone prior to combat. I doubt he will ever do that again, because it resulted in a bookkeeping nighmare. Haste, prayer and similar spells were cast, and because the enemies had SR as well, it required a multitude of SR rolls, and then we had to carefully record/remember who had what benefits.
And the party wizard getting affected by a symbol of insanity was a problem as well, because he was unable to 'voluntarily' lower his SR, causing multiple Heal spells to fail.
Often players tend to forget their character's SR when a beneficial spell comes rolling around, and often the DM fails to notice it as well. I would favor a 'choose freely if you want to use your SR against spells' option, just to reduce the number of rolls and the bookkeeping.