So I thought the Spirit Bomb wasn't meant to be able to hit good guys? So if Jiren is a good guy which as far as we can tell he is, and Goku has no reason to think he's bad, why would he use the spirit bomb?

Perhaps, he was repeating something that has happened before, perhaps he knew he could not defeat Jiren with it, but actually intended to absorb it. The look of surprise could simply have been awe at how much energy and power they added into the bomb from putting everything into it as they pushed it back and forth, before it turned to determination as we saw to have his plan fulfilled.

I have a gut feeling that Goku knew what was going to happen, that he wanted to use Jiren to add power to the spirit bomb, which was see from the way it expands, contracts, and expands again as they clash, before it collapses into itself. The only reason why it would collapse onto itself is if it had enough energy in it, and if it had enough to begin with it wouldn't have collapsed like that.

I guess the only thing that Goku didn't expect is how much power he would receive from it, and how much it would affect him.