"Hey buddy, do you mind if we pause the game for a minute so I can plan how to best intercept that attack fleet you're sending at my homeworld? Thanks, you're the best!"
Somehow I don't see it happening in most cases

It works in DefCon though. Players can vote for a game speed or full pause. I suppose it works well because the game lasts only 20 minutes at most and is divided in 3 distinct part (Defcon 3: place ground and naval units, Defcon 2: order your units around, Defcon 1: nukes allowed).
But yet it works, so maybe it's possible to implement a temporary slow-mo request in the game for players who feel rushed. Maybe this can take the shape of some kind of time-shifting device that eats up a lot of ressource for a short time. I'm sure it can be implemented in a consistent way.
Of course, this breaks the pace of the game which is primarily a RTS. But regarding the scale of the game which is supposed to be epic, in opposition with skirmish games like Warcraft, I think it makes sense.
Yeah, I hate being rushed in games

In addition to Space Voyager post, I think open space travel could be counter balanced by attrition. I think Empire Earth (or is it Rise of Nations?) works that way.
When your units are out of your empire boundaries, they get higher attrition damage the farther they are from your empire. Concerning Sins, I think it could work well if attrition occurs only if your ships are out of your empire boundaries and out of a gravity well or phase lane. Attrition damage could be countered by supply ships or a specific technology (in Empire Earth/Rise of Nations --can't remember which one-- attrition is lowered or nullified with a specific ressource: citrus).
Of course, this have some implications regarding scouting and colonisation that need to be worked out.
Btw, I wonder if empire integrity have any importance. I mean, is there some kind of consequence when your empire is split in half ?
NOTE: I pre-ordered a few days too late for being in the beta so I did not play the game yet.