You can't use Wondertomb on Wi-Fi without hacking--it's totally impossible to have, period. Pokemon with 4th gen TMs/move tutor moves, however, are perfectly possible to get and transfer over, so there's no problem, as long as their used in FC matches and not hacked to be forced into Random Wi-Fi battles. The fact that they're banned on random Wi-Fi is completely irrelevant in a FC match, where there are no such bans and you're able to use them just fine, without hacking or anything. Under your logic, in DP, because of Petit Cup options, we shouldn't be able to use any Pokemon period in any of the modes that don't conform to those requirements, because that would just be like using a Wondereye and is just breaking its rules all the same...
Sorry, but that doesn't make any sense whatsoever. The rules of one option for battling (Random) do not extend beyond that option to others (FC) and there's no reason to act like they do.
Edit: It seems there was quite possibly a misunderstanding here. According to what we've heard, it seems that it may be the case that in Random Wi-Fi battles (battles conducted without friend codes) may have these restrictions on what moves a Pokemon may have. However, that's just that one mode/battling option--this does not seem to be the case in Friend Code matches, and you appear able to use any legal Pokemon in them. Therefore, as the 4th gen TMs/move tutor moves themselves are perfectly legal, and we're still able to use them in Friend Code battles, there doesn't seem to be a real problem here to my knowledge--the Pokemon themselves aren't hacked, and they don't need to be hacked to get online or are prohibited in any way when doing a Wi-Fi battle through Friend Codes, so it seems perfectly fine to me, and I don't see how any comparisons to Wondertomb are warranted here.