In Marvel Comics there are multiple versions of many of the characters and that's thanks to the in-canon plot device of there being multiple universes and therefore, different versions of characters and stories.
The main Marvel Comics universe in the books is the 616 universe; the Ultimate Universe (where the Samuel L. Jackson version of Nick Fury was introduced) is designated 1610. Even the Marvel cinematic universe has a designation of 199999. Pre or post-death Coulson (or both) could be from alternate realities. Heck, even the entire Agents of SHIELD series could be written away as a separate universe than the films if they can't maintain continuity with the films.
If Guardians of the Galaxy follows the Marvel Comics, even it could take place in an alternate future.
Verdict: It's too early in the franchise to start branching out into other universes. We've not even explored this one yet.