I don't think that Jet2 in Manchester will threaten the LBA operation.
At first I was surprised, but this could be a smart move, it establishes Jet2 as a Northern operator and their reputation for service is already well known in the North West. Although EZY and FR are at Liverpool, it keeps them out of direct competition.
Also I think BMI Baby may have a limited lifespan at Manchester, I can see some of their routes going mainline to feed the increasing longhaul destinations and the remainder could become easy pickings from Jet2.
Good luck to Jet2 in Leeds and Manchester I say.