It's probably too obvious, but I think I've come up with a reasonable and elegant solution: By its very nature, the bridge and walkway will be elevated above ground level. Why not use that ground level space right at Harbor Blvd for an additional security checkpoint, with some vertical circulation (likely 2 escalators, 3 elevators, and stairs) up to the walkway above? It would keep everything on Disney's property and would still allow easy access from the existing facilities along Harbor Blvd.
Assuming the walkway will slope at a more-or-less constant rate to provide 14' vertical clearance over the road (16' clearance in the center lanes for trucks), the first 260' back from Harbor will at have least 8' clear (typical ceiling height) giving them over 22,000 SF of usable space down there (nearly the size of the Soarin' building for reference, or about 2/3 the size of the proposed Eastern Gateway security checkpoint)
Yes, it would have some staffing and maintenance needs, but if Disney is so desperate for the additional theme park space (which would also need to be staffed an maintained), I think it's reasonable to expect they could operate another checkpoint here. If not, they should be forced to keep a new ground-level checkpoint on the existing Harbor transit plaza, which would also require more staffing. Disney has gotten some great deals from the City recently; it's time that the City pushes back and gets something reasonable from Disney
I imagine Disney has plans for this space (World of Disney east?) that they haven't announced yet. It's crazy to think that Disney spent over $20M on the parcel to only use it as a walkway. So why not get a little more creative with the solution?