That ultimately is every GM's bruden - keeping the game in balance, providing an interesting story or interesting framework for characters' stories, and not getting bogged down in the details of it all.
NJW is somewhat right in that characters that get too powerful can become powerful monsters, but there is the risk of having the character become that powerful while retaining a comfortable faith cushion, which is why I suggested the faith drain modification idea - tweak how quickly they become demonic.
Of course, over the long run, punishing "good" players for success is bad, and having characters who are weak due to their players constantly getting there characters in trouble should be taken into account as well. "Oh, player a has lost one character and built on that experience to fashion an interesting character who is holding her team together, and player b is on his sixth Leroy Jenkins, crying 'nerf naow'? Poor, poor Leroy, looks like he'll be on his seventh soon."
As for game bloat, well, either decide early that there will be a hard cap, either in missions, bases, number of characters, days weeks and years, or number of players, and stick with it, or go with the flow, and if things get a little derailed but everyone is enjoying it, let it be. Sometimes our creations take on a life of their own. the trick is to manage the growth so it doesn't become cancerous.
faith amulets. In the base camp, or even outside the city altogether, let a PC "pray" over a given number of faith amulets for use on missions. "Pray" over ten low power, one shot ones, or two high power, reusable ones, or one semi-permanent one with a specific effect.