Why do you think that bmi pilots would have a problem with LHR slots being used for longhaul? Think for a minute: 5 crews needed per shorthaul aircraft; 10 crews needed per longhaul aircraft. Shorthaul aircraft uses about 10 slots per day; longhaul uses 2. So if bmi LHR supports 20 shorthaul aircraft (let's say 200 pilots), it could support 100 longhaul aircraft. That's about 2000 pilots. Yes, that's right - multiply the number of pilots required by 10!
Almost regardless of the seniority deal that is achieved, anybody in the combined airline will do incredibly well out of it. An "asset strip" would not be the nasty sort of thing you see in shorthaul takeovers - it would be fantastic! Most bmi pilots would love to see this happen - in the interim you get the best of both worlds (cos the 100 longhaul aircraft ain't going to happen overnight - or even in a decade, I would think!) - and people will be sufficiently senior to bid for what they want within a few years.
Of course the slots at LHR are the most valuable asset - of course they would be used as such in the event of a merger/takeover. However, you are stupid if you think that the pilots would lose out as a result. bmi gets unrestricted longhaul with its slots. Virgin gets control of 19% of LHR slots. The only thing that would lose out would be .... BA! - who would find themselves with a competitor who has the ability to take them on in any longhaul market they care to.