Because at the time Madoka, while she may have regained her powers and memories, wasn't omnipotent.
It also implies that the isolation field is actually blocking Madoka's omniscience, since she cannot enter the isolation field as a concept.
Source: Rebellion/Synopsis - Part D (2nd paragraph)
[Homura] then grabs Madoka's hands, surprising her. (It is implied that Madoka has not regained her omniscience because she is still existing in only one place.) Homura says that she's finally caught Madoka as her soul gem goes completely black.
Source: Rebellion/Synopsis - Part E (5th Paragraph)
Now we can assume that had Homura not interfered, Madoka would have regained her former omniscience, but while she was in the Isolation Field we don't know exactly what effect this was having on the universe.
- Maybe when Madoka recovered, she could then attend to any witches which may have been born while she was away
- Maybe before leaving, she had a backup system in place to keep the status quo until her return
- Maybe as a token of appreciation and worship, the Puella Magi saved by Madoka would detain Witches with some form of magic until the return of their Goddess
How was Madoka not able to take Homura into the Law of Cycles since that's what her wish was in the first place?
Now, more than likely what happened was that Homura created a major Paradox preventing the Law of Cycles, a law of the Universe, from doing what it was meant to do. We have seen a major Paradox like this before when Madoka made her wish, became a witch that could destroy the universe, yet was able to destroy it as well and continue fighting on. I suspect a powerful enough paradox will cause the universe to "reboot", creating a new rule to account for the Paradox as it did with Madoka's wish.
How can a soul gem be tainted by anything but grief/despair?
Because Soul Gems are the Magical Girls themselves. Since despair is a complex emotion of hopelessness, anguish, and unhappiness, it seems perfectly logical that a Soul Gem could be filled with Love as well.
As for it being tainted with love, you should read over this answer which suggests how Homura's love became tainted, to quote one line
Homura claims that all this negative energy comes from her love for Madoka due to several events:
[Homura] became a demon
Just to correct you here, she's a self-proclaimed demon.
Homura says that since she is a being that brought down and imprisoned a god, it's only appropriate to call her a demon.
Source: Rebellion/Synopsis - Part E (6th Paragraph)
Homura became the same as Madoka, but the difference between Madoka and Homura is that Homura manipulated things so that she would still exist in the universe in the same way she allowed Madoka to as well (albeit without her memories or powers)
Homura, now wearing an earring and lacking her magical girl ring, claims she only took a part of the Law of Cycles — the part that was Madoka before she stopped being herself.
Source: Rebellion/Synopsis - Part E (7th Paragraph)
So in a sense, Homura and Madoka are the same. However, Homura proclaims she is a demon because she is the opposing force to Madoka's will (the Law of Cycles) by breaking it and we see at the end that should Madoka remember who she is, the Law of Cycles will reclaim her which Homura will do what she can to prevent.
