I could read your question in one of two ways - how do we punish the Eidim Zomimin, or why do we punish them as we do, since it's already Ka'asher Asah - and so I'm going to try to answer both in one shot.
Mishnah in Makkos 2a (translation that follows is my own free translation; the brackets are my own addition to help understand the Mishnah):
"How are witnesses turned into Zommemin [yet don't receive the punishment they tried conveying onto the defendant - Gemara]? [For instance, if the witnesses said,] 'We testify that Ploni is the son of a divorcee or Chalutzah,' we don't say that [the witnesses] should become children of divorcees or Chalutzos instead of him [since they're also Kohanim - Rashi], but rather, we give them Makkos. [Another case: if the witnesses said,] 'We testify that Ploni killed b'shogeig,' we don't say that [the witnesses] should be exiled [to the Ir Miklat] instead of him, but rather, we give them Makkos."
Perhaps one could infer from here that there's a difference between a punishment imposed on a person and a status change imposed on a person. What both of these cases have in common is that the status of the person changes, from a Kohen to a Challal in the first case and from a free man to a ben Golah in the second case. Thus, one can't give them the punishment they wanted to impose on the other person, because there is no punishment. Thus, there's no issue of Ka'asher Asah, because they never caused anyone to be punished!
Ay, you'll ask me, why isn't Ir Miklat considered a punishment? According to the Rambam (Moreh Nevuchim 3:40), there's no issue, as the entire inyan of Ir Miklat is for the benefit of the family of the deceased and not to punish the murderer. But even according to the Sefer HaChinuch (410), who says that it's to show the murderer that he must be more careful with how his actions impact other people emotionally, you could still argue that it's not a punishment, per se, so much as a lesson prompted by something that he did.
If you think that it's a little far-fetched to say that there's a difference between punishment and change in status, I'll bring you a proof from the rule of kim lei k'dirabah minei. As we know (IIRC it comes up in Makkos 4a-b), if a person is obligated in multiple punishments, he is only given the worst one. Thus, if a person kills intentionally, chas v'shalom, and, while he's at it, damages the victim's clothing, he is patur for paying for the clothing, since he's chayiv misah.
Now, what about the Oneis, Mefateh, and Motzi Sheim Ra? All of them are chayiv to pay a k'nas, to pay the boshes and p'gam payments (at least by the first two), and to marry and never divorce the victim. Now, I understand that payments can be merged into one "punishment" for the sake of kim lei k'dirabah minei. But why does he have to pay at all, since he's forced to marry her? Perhaps it's the same concept: only the payments are considered punishments; the requirement to marry her is a change in his status from "single" to "married."