I recall Dragonstar and the discussion we had about elite kamikaze agents spending their time dead, being Resurrection True-ed when needed and deployed again as deep probe suicide agents. All you need to resurrect them is their "social security number" or other unique identifier. The time between missions is spent in their alignment's version of "heaven" - even demon lords could make pocket paradises for such people to spend their "dead time" in, just to keep the agents willing and viable. A very scary angle on the Hassashin theme.
Yep, there are lots of interesting plot complications that arise in a world where the soul has a social security number, and where there are galaxy-wide insurance companies...
(For a SF novel view of resurrection-suicide-stormtroopers, I recommend Glen Cook's "The Dragon Never Sleeps".)
Other complications that arise if you have resurrection, combined with an assured heaven/hell destination are:
A) Evil people are sent to the hell or the abyss. There, powerful bad people tend to turn into more powerful, more bad devils/demons. These wage war on the rest of Existence. So, isn't killing bad people actually just making things worse for you? And would not redeeming, rather than killing them, make things better? A war for souls, not for bodies...
We had an interesting twist on this lately - the Campaign Big Bad had marked all his subordinates with an indelible mark, and when they died, their souls went to make him personally more powerful. Unfortunately, the writers of the adventure path had made very little of it, but at least there were some interesting discussions.
B) Similarly, good people are sent to heaven, and you know it. So, why don't you simply do a Jonestown when things in this world starts to go a little sour? "Oh, an orc army approaches... where is the Cool-Aid?"
And, besides resurrection, there are ways for the baddies to return ever worse, such as coming back as undead, devils or demons. A risk that makes capture and imprisonment really attractive compared to slaying...
Which in turn begs the question why a hero couldn't come back as an angel (or other good outsider), rather than being merely resurrected. You know, the whole Gandalf thingie....
As a DM, you can explore these things, as a means to make things odd, surprising, and give you an opportunity to play around with the players preconceptions. Or you can either do an "don't ask, dont tell" or outrightly forbid these things, to stop things from straying from the comfortably normal.