SR is an "outer layer" of defense against magical attacks, the "inner" ones being saves and eventual energy resistances the creature may have. It's usually a natural defense that works even when the creature isn't aware of a magical attack.
Therefore, Spell Resistance check must be rolled first. The spell resistant target can drop the SR as a standard action, in which case any spell cast on it will function normally, possibly allowing saves.
For a spellthief to absorb a spell, the spell must be on the verge of affecting the character, which it won't, if the spell doesn't penetrate the Spell Resistance.