What do you mean always running? Nothing is running unless the watch is on and you're presumably looking at it. When I use a stopwatch on my iPhone, I sometimes forget to stop it, and the next time I look at it, it reads 24 hours +, but it hasn't been running in the background burning power ... When I leave the app, it stores the time in memory, then when I recall it, it references the current time, and the stored time, and updates accordingly. A watch complication would work exactly the same way.
Why it would have to be especially complicated to sync to minutes is beyond me, but then I'm not a programmer. I regularly use ProTools and time sync is very important, yet somehow, I'm able to keep various devices in exact sync, against a locked time code. So I really don't see any issues here.