I am in the Air Guard and also fly commercially. I was with ATA from 1996-2002 and then some of the non sched under belly MIA operators. The Guard has been the place to come back to when the wheels fall of the part 121 bus. I have been on a continuous MPA tour for over 2 years flying in support of the Afgan/Iraq mess. I can't tell you how grateful I am to have had the Guard to bail me out. In all the years I have been doing both I have seen some commuters be gracious with military time and some not. Most of it depends on how you play the game. If you drop orders on the airline all the time short notice then they tend to not play nicely in return. ATA was a great place for military time. I faxed them the UTA order for the year in advance and I tried to bid accordingly and they met me half way. I worked for a while at Amerijet in MIA and even with an order faxed/hand carried/and mailed they still made it as difficult as possible. Then charged me double the sick call time for the time I missed. One pay period I actually flew 54 hours(65 hr gar) and was paid for 45 hours after they deducted 5 hours a day for the 4 I missed for the military. To this day if I ever see them get a goverment contract I will be writing my congressman. Anyways the best bet is whatever works for you and your family. If you work for a commuter and are based at the same airport as your flying unit you got it made. I know guys who are on reserve and are at the Guard doing RUTA/AFTP's on the same day. I now am in ground school for a 747 operator and hope this one works out. If not I might have to give up and become an AGR fulltimer. Even though I much prefer the lifestyle in commercial aviation the AGR gig pays much more than 90% of anyplace you can work anymore. If you have anything else PM me.
Best of luck to you.