Allowing it for 1v1 MP would be a great start, and yes that makes things MUCH simpler. However I don't think it has to stop there. Here are some considerations (I will apologize in advance for the long post):
First there seems to be a notable amount of support in the FOG2 community that looks at Empires as a fresh take on generating MP battles. I don't have any demographic data on this, just my opinion.
Next, regardless the number of MP participants in a given campaign of Empires, if all players have the same understanding about porting battles to FOG2 then there should be little issue with turn times. A key point here is that I don't foresee every battle being played out using FOG2 (though players would have that option if they want). I foresee only those few key battles in a given PvP war to be played out....and that would require mutual agreement by both belligerents. If players do it right on the strategic level, then most battles will be so lopsided that they won't be interesting to play out. Using FOG2 for battle resolution would be based on 1) player preference (they may or may NOT want to play it out); 2) A quick discussion whether or not player schedules would allow for resolution "Hey Bill, you got time to play this battle out?".
Regarding battles against non-player countries (NPC's), there are probably a number of FOG2 generals who would like to participate in a "mercenary" mode whereby they only act as the general to fight out the FOG2 battles without being part of an Empires campaign. Use of the "Challenge" in FOG2 for MP battles would enable this. Empire players can issue passwords to limit who accepted these challenges.
The following are some design concepts that could be incorporated to help smooth out Empire turn resolution concerns:
Restrictions could be placed on the time allowed to finish a battle using FOG2; if battle time were exceeded then Empires would auto resolve that battle instead and move the turn along.
Concurrent battles: WEGO allows for the possibility of multiple battle notifications to be sent to players at the same time. With all players establishing their moves, the computer will be able to predict most battles (but not all) and when/where they will occur. Notifications can be sent to affected players and they can make their decision for auto resolve or FOG2. Then multiple battles can be fought concurrently to help keep things moving, as well as engaging as many players as possible.
A checkbox option could be added to the End of Turn sequence that would prevent battle notifications for player vs NPC battles. I.e. auto resolution for PvNPC battle instances becomes default for that player each turn the box is checked. This means the selecting player would only get battle notifications against other humans, otherwise that turn keeps moving.
A checkbox option could be to the End of Turn sequence indicating a players preference to *only* use auto resolve for that turn. It can be altered from turn to turn according to player preference. When only using auto resolve the game knows to not even bother that player (and his opponents) for battle notifications further reducing turn interruptions.
Develop a simplified method of comms for players to make simple game decisions during turn resolution. This could be something web-based, text message, email message, a simple mobile app...basically anything that would allow universal access by mobile devices to enable quick decisions to facilitate turn resolution over the course of the day without a person being in full-gaming mode. Example: responding to a text message at lunch saying "Battle Alert: Impulse-3; Region-Apulia, 10 Width; General-Hannibal, 16 units vs Roman with 20 units" Obviously this is just a crude example to illustrate the point. Anyway, players get the notification and can make a quick binary decision on what they want to do. Hit the Play Out action or the Auto Resolve action, then move on.
Bottom line: you would give players maximum flexibility in their gaming experience to make it what they want. I primarily see myself playing with 4 or 5 other people I know who have similar ambitions with their gaming experience, and I estimate most other users do the same.
Anyway, I just wanted to throw some considerations out there because I have given this a fair amount of thought.
I think there are reasonable methods to help reduce Turn interruptions to a level acceptable to those involved in that campaign. This is an option I would even be willing to pay extra for.