^^^Plot expediency and time constraint.
Possible explanation: the governor being good friends with master Vrook Lamar could have done a great deal to aid them. Resources and even hire for those now grateful for Jedi presence after fighting off mercenaries. If you think about it, khoonda was a trade hub attracting people. It isn't much of a stretch to say that one area with a good economy might have drawn other help. Granted it's a minor detail, but I agree it would have made the story a lot more plausible.
Perhaps rebuilding has exhausted the masters to a point that they could not sufficiently defend themselves?
Aside from being irreparably damaged (implied by the dialogue of the Jedi masters), you have both exposure from Malak's attack, and residents who still didn't like Jedi. Sure the Exile did a great deal in her efforts, what with fighting off the mercenaries, but you will inevitably have the percentage of population that "doesn't care what the Jedi have done just so long as they are mostly gone".
As we're learning, Tython, Tatooine, and other places are going to have enclaves of their own.