Well, there's no real penalty for buying it now or later, it doesn't matter.
If anything, I suggest buying factions now, to atleast have some more skills at your disposal.
(Ofcourse, if you're a person that likes to finish stuff, then by all means, finish it first.)
Well, the only real thing I was worrying about was that if I don't finish the missions on Prophecies and start missions on Factions I'll have a big space in the story =/
There won't be a space in the story as factions is a separate story to Prophecies. The only gap you'd get is the memory gap between where you left prophecies and when you finally come back to it...