I'm going to be a bit finicky for a minute. Let's not simply say "she became" a devil. Through deductive reasoning, she arrived at the conclusion that the only thing that could match the power of a god (and take them out) would most likely have to be the devil, hence she assumes that status.
The Madoka in Homura's world is still the same Madoka (flesh and blood) whom she just ripped the god power from. When she recreated the world, her friends got brought into it.
Unsure about the love bit. Kyubey's species is... I don't know. I like to think the Incubators have not been eliminated as that would deplete all chance of a follow-up, which there still is potential for (imho). What I think we saw was the Incubators being forcefully given the ability to feel emotion and pain for the first time, hence the cringing.
I think Homura has wiped their memory of knowing they are witches. I'd think they still are, just like how Madoka still has her god powers. The circumstance is that so long no one remembers what they were, their powers remain dormant.
Yes, Kyubey's goal was to control Godoka. Madoka wanted the Incubators from harvesting energy obtainable from dying magical girls, so she changed up some rules (by recreating the universal rule of their life cycle), but then the Incubators just worked around it to find some way to still continue to harvest energy. This time, they can just harvest it from Godoka herself.
Could theere be another season? Orobuchi did a great job with the ending. Even if there won't be, he leaves it off hinting possibilities. As much as I don't like when things get turned into cash cows, I actually don't mind if he does another sequel.
Madoka is only a "threat" in that she can easily reverse everything Homura has done to accomplish what she did by the end of the film. I'm sure you wouldn't want people undoing all your hard work. That's how she is perceived as an enemy to Homura. The beautiful part of this relationship is that they are still best of friends so the struggle to find mutual agreement is why the plot is now so fascinating.