Since TBC is current content again, we can discuss this with relevance.
The main justification in TBC is built on three principles:
1. Garithos
2. Fel usage
3. Night Elf rivalry
Garithos
Garithos was used as this great betrayal, to spur the Blood Elves to leave the Alliance. Okay fine, leave, maybe? This was a rogue general the Alliance disowned in a time where there wasn't much they could do to reign him in. This was also a general that was fighting an undead apocalypse and some of the blood elves he attacked WERE NOT INNOCENT. At most, really, this should have been justification for re-negotiation of certain aspects of the Alliance.
Garithos was also FROM LORDAERON AND ALLIED WITH UNDEAD. Why in the hell do proud, xenophobic, anti-undead Blood Elves not see that on top of the fact that the Forsaken are a corrupt and vulgar race (in their traditional views), that these are the people of Garithos. Not Stormwind.
If anything, this is a sign for Blood Elves to rejoin the Alliance, now that the fiercely anti-belf population is gone. Not go side with them and blame people thousands of miles south.
Fel Magic
Both factions hate Fel. But the Horde is especially suspicious give Orc history. It shouldn't need elaboration that the orcs are incredibly weary of the Cleft of Shadow already, and are forced to accept them due to the political reality. Allowing in Blood Elves bolsters their sympathies, when the Horde is doing everything in its power to limit fel magic.
Night Elf Rivalry
This one might make sense, especially with the Fel Magic. But really it is not justification to join the Horde, its really just one point against them joining the Alliance. In all honesty though, the Nelves are allied with the Arcane using races of Azeroth. I don't see why they can't see the Belves joining as a good thing; Keep these rivals in check with peoples who can actually engage with them on an incredibly intimate level and therefore monitor their activity. And obviously the Vanilla Alliance showed the Nelves were less suspicious of the Arcane to some degree than implied. Plus, they're seemingly fine with high elves, who's non-fel disagreements and histories with Night Elves are near exactly the same.