I was wondering if it is possible to add factions to companions through the console to prevent them from attacking evil factions. Mainly like the Dark Brotherhood and vampire factions that the player might not wish to attack because they are a part of that group.

Do you think something like ModFactionReaction 100 would work to stop the attacks?

It might, but using SetFactionRank FactionID 0 would be better.

EDIT: Responsibility may also be a factor. A companion with a responsibility of 100 (which most have) would automatically be hostile to "evil" factions. You can change this by typing SetAV Responsibility 0 in the console, with your companion selected.

I believe some of the companion mods already have the companions join factions with you, so it may just be a timing issue for those. If you added the companion mod after joining, they may not be in sync. However, I'd have expected the readme to tell you what console commands are needed, or to provide another way to match up the player with the companion.