As far as canon goes, nothing in True Resurrection says it doesn't create a second body, and you're the GM, so that's all you need (and you don't even need that, really).
As far as headaches, in theory a player might argue that you are violating the rules, and how dare you? But I don't think that's likely from what you say about your group.
Violating suspension of disbelief has been mentioned as a possible problem as well, but if true resurrection and creation of undead doesn't bother your player's sense of disbelief in the first place, I think that if the combination of the two does then that's just a little too idiosyncratic for you to be expected to predict it in advance. I would see this as more of a demonstration of the strange possibilities allowed by magic, and a sign that you have a world deep enough to have an internal consistency that doesn't match that of the real world.
If the body created by True Resurrection is destroyed and lost, the undead created out of the original body is destroyed and recovered by the player characters, and they try to use a Resurrection, then you may have another question to post :)
I wouldn't let an idea that you think your players might like be squashed by undue squeamishness about violating a rather grey area of the rules.