That's a risk any investor takes. You're assuming AL will go bankrupt. Based on the profitable nature of the business that seems to be a small risk, though, like any firm, the risk exists. The staff are more likely to be happy to see the back of mick as the scenario of him winning offered the cast-iron guarantee of being fired. A small risk of AL going bankrupt vs the 100% chance of being fired... I think the desired outcome has been reached.
If FR takes over EI, you can also be sure that EI employees will lose union representation and suffer from worse pay and condtions than what they currently have...
Remember the IRL-UK market (largely DUB market) has changed a lot since 2006/7 and routes once profitable are now heavily loss making.
Why are FR will operating them then?
Imagine that somehow FR gets the green light to take over EI. BA gets the lion's share of the Heathrow slots and flyBE takes on 20 routes out of Ireland (including, incidentally, some longer sectors that really need 150+ seaters rather than E195s). What happens three years down the road? BA shifts most of the Heathrow slots over to more lucrative long-haul, and FR goes after flyBE with aggressive pricing and chases it off most or all of the 20 Irish routes, just as it's doing with Wizz in Cork. Result: the Irish market is then a Ryanair near-monopoly. But consumers should rejoice because "Irish aviation is even stronger"? Tell me again how exactly? 
BA will still have less (in proportion and in overall number) than LH in FRA/MUC/ZRH and AF/KL in AMS and CDG even after buying EI's slos
If the Irish market becomes a FR-monopoly and then raises fares, then maybe BA/BA CF (after buying WX) could then cut raise the stakes in the competition on LON-DUB (FR are not interested in LHR-NHD)
Could Flybe least some A320s off BA for the irsh routes then?