Now, I'm a complete outsider in all this, so I might say something completely idiotic here, but:
Shouldn't it be down to two people: nage and sensei? If your Sensei decides that it's best for you to train with resistance, then you both start training with resistance. If Sensei has no word in the specific matter, I'd say it should be up to nage, who is practicing his/her technique, then he/she can either ask for more resistance to test the technique, or less to refine the technique.
I will however quickly say, that resisting a throw/lock/whatever wouldn't automatically lead to injury, as some have stated. Unless you are some crazy doped up person, your body would naturally give out long before any of your joins or bones break (which is why the techniques are also useful in the first place). I can't see how you could break a join, unless either an accident happens, or someone is deliberately trying to break a joint. It's not like you go "I'll resist this.... whoah my arm broke out of nowhere, where did that come from?!".
Granted, I so far only have experience (3rd Kyu) in Shotokan Karate, which is obviously very very different from Aikido, but really... joints and bones don't break out of nowhere