Well, it's rather easy. You have to stop thinking in terms of "allies"
In 7e, you build your army from separate detachments. One of them is Allies Detachment (AD), but noone forces you to use it, if you want to include units from different codex. Usually you'll use Combined Arms Detachment (CAD), which consists of the usual Force Organisation Chart. Rulebook does not know any other detachments, so for any other specialities, you'll have to look into your codex / dataslate / White Dwarf / Imperial Armour etc.
You can build your army from CAD Eldar and CAD Grey Knights, for example. Or, similar army can be build from CAD Eldar + AD Grey Knights, although you won't be able to use your Grey Knights HQ as Warlord.
Now, Assassin in their dataslate are used as a separate, unique form of detachment. They can't be used as any other known detachment, because it's simply impossible (as you said - no HQ, no Troops... that prevents you from using CAD Assassins or AD Assassins).
So don't bother with FOC. Just add one or more Assassins to your army. Allies Matrix in the rulebook gives you rules, how they will interact with the rest of your army. So if you use CAD Eldar, for example, and add your Assassins (all four of them, for example), no problem - just keep in mind, that the Eldar and Assassin part of your army will treat each other as (I believe) Allies of Convenience.