It seems doubtful that the expansion will happen after the explosion on Citadel 17. It already seems hinted, and is mostly speculated that the Alyx expansion will take place before Gordon arrives, probably to avoid all the plot intigues that the end of HL2 opens up. What the end of HL2 may have done, is kill off certain very important characters - why on earth would they answer the questions the audience have in an expansion pack that not everyone will buy?
Besides this, the convention for Expansion packs in the HL universe is to have them running alongside the original game: even the lengthy sections after Gordon has gone to Xen aren't necessarily after Gordon defeats the Nihlianth, as Marc Laidlaw himself has pointed out.
