Thanks for bringing this up.
Yes, an Assist Trophy is the ONLY way so far to COMPLETELY rule out a character (along with Pokéballs, being the Pokémon version of Assist Trophies). I personally think that boss characters will probably not be unlockable to play as either based on a couple things I see with Petey:
1) The way he attacks - It's been stated that he's going to attack with cages holding other characters, and that to beat him you have to attack the cages. This isn't even standard Smash fighting (more like fighting Master Hand), and I don't know how that would translate into gameplay. If they have an entirely DIFFERENT moveset for him without the cages...well, we've yet to see that.
2) Size - Petey is, by far, the largest character shown as of yet. I think he's even bigger than Giga Bowser...sure, they can scale him down, but...then why ever make him that big in the first place?
3) The way they updated him - He's got a very unique looking update post. Instead of having a blue gradient background, he has a pink one. I suppose all the bosses they reveal will have this same background format. If he were going to be a playable character that you happen to have to fight in the game, then it would have made more sense to update him with a normal PC character post first.
Now, none of these things are PROOF that bosses aren't going to be playable since Sakurai never said so on the site. But I think it's reasonable to assume as much at this point in time.
The vast majority of other reasons characters have been "deconfirmed" on this thread boils down to nothing but speculation, which isn't really a deconfirmation of anything at all. If it's going to be done that way then fine, but there should really be a lot more "critical condition" entries like Lip's on that list than actual deconfirmations.