If he was still in the RN and was weekending, then you would still be paying the food charge and mess bills, and some travel I assume? The difference is that you are now paying a mortgage instead of rent on MQs.
I'm a SAHM, but I wouldn't say I have no control. Finances are joint - he earns it and I spend it!
Take his cards off him. Set a reasonable budget for travel, rent and feeding himself whilst away, plus a little extra for a pint or a takeaway perhaps, and set up a new account that has no o/d on it. That is his money for the month. If he runs out tough shit.
You have your housekeeping or whatever and presumably you can live within that. Have another account for mortgage and bills and put a sum in to cover those and no more. It's a bit like the tin my gran used to have where she kept money for the electricity and gas etc, but with bank accounts.
If the account with the o/d is joint, and any of the cards, you are liable as well as him, so even if you split up, then you will still have the debt.
You need to be perfectly calm when he is next home, very grown up, and tell him that you need to discuss this rationally with him. Draw up a plan for dealing with it together. Don't do the grand flounce of it's all over as that will just set things off again.
I have a big bill to fund for work that needs doing on my house. Christmas will be pared back present wise this year to cover that; and with the Belgian car tax bill rapidly approaching (2k plus), then we'll be eating out of the freezer in November.
Explore renting out and moving with him again, I can let you have the name and number of my letting agent - she's brilliant.