If the deal is already pending, you probably don't have the option to make a counteroffer anyway, so your only option would be to protest. I don't think I'd protest this one (as tallmike says, it's not ridiculous) unless the commish was taking unfair advantage of a newbie to fantasy baseball. Otherwise, I wouldn't protest formally, but you may wish to ask either team for their reasoning here, and remind the commish that he or she should be even more careful than the other owners when making trades that might appear lopsided. That way, you wouldn't make unnecessary waves now, but perhaps improve your league in the future.
Anyway, that's just my two cents. I'm always extremely hesitant to formally protest or veto deals unless there's something truly shady going on; if your league has other standards, this may not apply.