That's the thing: she was basing her actions always on previous Madokas. When confronted with the final Madoka, the one trying to save her from becoming Homulily, she did little to find out what she truly wanted and took the same radical attitude she'd developed when try to save previous Madokas from Walpurgisnacht.
Previous Madoka's are the same Madoka with her memories erased. If you want to treat other Madoka's like their opinions don't matter then Madokami is no different, Madokami was just another version. She literally asked Madoka what she wanted, she wanted to stay with her friends and family. Take away the knowledge of the suffering of magical girls as they turn into witches and Madoka wants to be back home with everyone. Homura is just doing what Madoka asked of her.
Homura's time magic was incidental to her wish to save Madoka. Since she was now in a rewritten reality where Madoka couldn't die or become Kriemhild Gretchen, her magical girl powers would naturally be rewritten as well. And it's not like Homura wouldn't have met Madoka when her work on earth was through.
We know that Madoka has the power to rewrite powers and wishes, she explained to Sayaka that she chose to keep Sayaka's wish intact. Madoka had control over whether or not Homura kept her initial wish and thus her power. Homura has no idea what that means to be taken by the cycle. Do they cease to exist, do they spend eternity with Madoka, or do they go to magical girl heaven where everyone gets cake and ice cream? There was never a guarantee that they would be reunited again. Also there is homura's need to make Madoka happy, is she happy to be forgotten by her family and friends? Most likely not, even if they spend eternity together that doesn't mean that Madoka is entirely happy with it.
If Homura merely "saved her from having to live forever like that", she wouldn't have sealed Madoka's memory and trapped her in a false reality. She might be "justified" in splitting her from the Law of Cycles, but beyond that Homura is effectively denying her right to her own agency.
First off, why call it a fake reality? It's just as real as what Madoka set up. Secondly, she sealed Madoka's memories because if she didn't she would rejoin the law of cycles. And denying her right to her own agency? You mean like she has pretty much done with everytime she went back in time and exactly what Madoka did to everyone in the universe?