My random thoughts after reading your post and those verses in Matthew
The parable says that the weeds will be gathered, bundled and burned first
...
they are teaching that true Christians must isolate themselves....
Seems clear which group they are in then doesn't it?
Then again, a few verses down Jesus said:
47 “Also, the kingdom of heaven is like a net that was thrown into the sea. It gathered all kinds of fish. 48 When it was full, they pulled it to the shore. Then they sat down, gathered the good fish into containers, and threw the bad ones away.
This time around the good product was separated out first or at least at the same time.
In both cases it was the Angels doing the work not some earthly organization.
In my opinion neither of those parables seem to indicate that the the bad fish and weeds would be the vast majority
Finally Jesus asks:
51 “Have you understood all of this?”
“Yes,” they answered.
We are still arguing over this today so I have a feeling that the diciples may have been a little quick to answer in the afirmative.