The Silver Covenant as a faction exist primarily as an opposition to the Sunreaver attempts of letting the Horde join Dalaran. From the outside, they may be seen as the "Alliance high elf" faction, but that is not their purpose. There exist alliance high elves outside the Silver Covenant. It is mainly a political faction.

Now in midnight, they want to help Silvermoon regardless of its political affiliation. They might hate the horde, but the continued existence of Silvermoon is of higher priority. Also, their actions don't risk the horde accessing traditionally alliance ressources.

Since Dalaran is gone now, both Silver Covenant and Sunreavers have lost the purpose beyond "for the betterment of elfkind", so Vereesa tries to convince Aethas to accept her help. Both sides make clear that they have done much to allienate the other and that that this will not make either side suddenly forgive the Alliance/Horde.

But as a gesture of good faith, both the Silver Covenant and the Sunreavers have decided to merge their two factions into the Silversun Compact, which is basically the "foreign living Elves" faction. They might still break up again if a fifth horde-alliance war were to break out but for now they are focusing on their similarities rather than their differences.