Cross-faction guilds are coming in Patch 10.1, but currently, you cannot play queued instanced content with other members on the 10.1 PTR and you can’t search for cross-faction guilds through the Guild Finder either.
Content creator MrGM in a series of tweets highlighted some shortcomings of cross-faction guilds and the Guild Finder on the 10.1 PTR.
First, the Guild Finder will continue to show Guilds where the leader is of the same faction as you. You can’t search or see guilds owned by the opposite faction, even if they have cross-faction members.
You cannot invite members of the opposite faction to your Guild without being in a community or Battle.net friends with them.
Probably the most-discussed topic when it comes to cross-faction guilds is queued instance content. Currently, on the 10.1 PTR, you cannot participate in queued instance content with your guild members in a cross-faction guild. Hopefully, Blizzard will allow cross-faction groups to queue together.
