I'm not quite getting why you can't fix this. (And, for the record, I agree with BMatthews...this needs to be fixed...more in a minute)

You say the hinges are glued. Fine. Cut them. But then you say you'll have "stubs" in the wings and flap. So? Why can't you just sand those stubs down flat with the flap LE and wing TE, and then remount the hinges elsewhere? As da Rock said...there's going to be plenty of room on that airplane to do that. If the hinges are "backed" by blocks inside the structure, then it's even easier...just cut out (if they're flat CA type hinges) or drill (if they're "peg" hinges) the old hinges away, and either fill in the slot/hole (hinge pockets would work well here if they're the peg type) or use larger hinges.

In short, there's probably a dozen alternatives here. Without having pictures, it's impossible to say which would be most advisable.

As for deciding to 'fly with some trim", be aware that what you've done is changed the AOA of ONE of the wings. This will induce both a roll AND yaw problem....the effect of which will vary with airspeed. In short, you're likely to find an airplane that "won't trim"...that is, it'll be "hands off" at one throttle setting, but "out of trim' at another...not an enjoyable situation with ANY airplane, but even more of a handful with a big warbird.

Now, in this case, your 1/8" PROBABLY isn't enough to cause many problems for casual flying...but it's really one of those "it'd be a quick and easy fix, why not get it right?" things.