I'm not sure it was ever implied that Minfillia becoming the Word of the Mother was part of any plan of Urianger's. he became involved after that point, when Elidibus approached him and he began to set up the double-cross.
Chances are he didn't specifically team up with Elidibus with the intention of sending Minfillia to the First, just to gain information on the enemy and potentially undermine them at a later date. When things then lined up so that he *could* set things in motion to do that he took the oportunity.
He's guilty over it because as has already been said, he acted without actually consulting Minfillia (or anyone else) on the matter, a move which essentially "killed" her from the perspective of a bunch of other characters, particularly Thancred and F'lahminn. She never did return from the first after all. Even if Thancred did eventually make it to the First and get to say more of a proper goodbye in Amh Araeng Urainger still essentially had his friend's adopted sibling sacrifice herself for the greater good. It was a betrayal of his friends even if it was well intentioned. He sent her to die.
You can also arguably trace the sequence of events that leads to her final "death" by giving Ryne her powers back to Urianger's intervention. She'd already sacrificed herself to become the Word but that's the work of gods; Hydaelyn called to Minfillia and Minfillia answered, but orchestrating her journey to the First? That's all on Urianger. If he hadn't sent her to the First she wouldn't have had to spend a century reincarnating and dying over and over again either. For all that Minfillia is relatively serene about it and doesn't hold a grude that doesn't mean he can forgive himself. Maybe if he hadn't done what he did something else might have come up later? Maybe he threw away a chance to free her from Hydaelyn in a way that let her live on? It's not necessarily a *fair* assessment of events but guilt rarely is.
Urianger's constant deceptions are a bit of a running gag at this point but it's always been a part of his characterisation that he's not just doing it for funsies, he'll act as a double agent or conceal the truth because he genuinely believes it necessary, that doesn't mean he enjoys doing it. Minfillia's sacrifice is sort of emblematic of that. He set up events which in the grand scheme of things were absolutely for the good of basically everyone involved; he saved the First from anihilation, gave the Warriors of Darkness some form of absolution by letting them help save their world after all, powered up Hydaelyn and made a figurative obscene gesture in Elidibus' general direction. But in doing so he hurt people close to him. Urianger's actions, even if they get him dunked on by the other scions on occasion do tend to pan out for the better, but it's not without personal cost.

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