Hey Ed,
I am in exactly the same position! I have two small girls 3 & 6 and my partner is a total c**k when it comes to my running, he snipes, moans and generally gives me a hard time about it, I now go to a running club where he seems to think we all put our keys in a pot and off we go,bumping and a grinding - he calls it the swingers club!
I am currently marathon training 5 days a week, trying to fit it in with looking after the girls and generally being a slave to the house (and his severe ocd) - This is why I love to run, it is a total destress. My partner plays football every saturday and trains 4 times a week - have I ever moaned at that no, its about give and take, but he cant see this!
My advice would be to just ignore her, and carry on what you are doing, especially if she does her own thing.
Can you run on a morning before work or during lunchtime or after work if you have showers there? I would just explain that you would appreciate her support, butter her up a bit saying I know this training bugs you but its only 12 weeks etc. Or get her to start running. You could also say as im going to be training lots why dont you have sunday mornings to yourself to do longer horse riding or some time out (obviously after you've done your run!!) yes it is time consuming but would she prefer to have a husband thats a fat couch potato?
Good Luck
Katy