I would claim.
The MOD will have paid you at the lower rate, 26p? for the journey to and back. For that you can claim the difference from HMRC.
For the intervening weekend claim at 45p.
Look at it this way. A civilian will travel to his temporary place of work and back every day or week. There is no presumption that he would remain away from home at a weekend.
Similarly, as a Serviceman within the civilian tax system, you should be treated no differently.
Suppose however you choose to remain at your deployed location and additional subsistence costs arose which were not met by the Service, extra messing for instance, then again you can claim these in the same way that a civilian would do so.
Provided you keep your JPA printout for that magic 6 years then you can counter-challenge HMRC. I was once challenged and responded with a breakdown of my claims. In so doing I noticed I had under-claimed. they graciously (b*ll*cks) conceded my claim was valid but declined to increase my claim
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non sinas bastardi tere te deorsum