Pistols are great if you want to be sneaky - they're relatively quiet, can equip silencers, and are pretty precise, letting you make headshots if you get up close to someone without being seen. SMGs, on the other hand, are great for taking down groups of enemies at close range, provided you don't mind everyone else in the area hearing you - they're loud, but powerful.
So I guess it depends on your play-style.
Can you be relatively stealthy with a pistol without using a silencer? I roleplay a lot when I play my RPGs, and the character I have in mind isn't one to use a silencer, but isn't one to go guns blazing either. Can I make a character that sneaks around, but also can start a firefight when **** hits the fan without being forced to shoot through the rest of the mission?
In short, can you get a good balance between stealth and firepower when going through a mission, or is it pretty much one or the other?