"In keeping with the many possibilities for the forces of the Ordo Malleus to appear within space marine and imperial forces, deamonhunters units can be included as allies in any of the following Codex armies:
-Space Marines, INCLUDING varient armies such as
Blood Angels, Space Wolves, *Dark Angels, Salamanders, and other loyalist Index Astartes Chapters
-imperial guard ect. ect.
*note that if deamonhunters are present the inquisitorial scrutiny means that the Dark Angels 'Hunt the Fallen' special rule is suspended"
that is direct from the deamonhunters codex.
the note isnt even applicable anymore

youre fine with taking the assasin. but did you also take an inquisitor? you didnt specify that, and if you didnt, then that may have been what your opponent was protesting. you have to take an inquisitor as well when taking an imperial assasin (not death cult, mind.)
but as for taking a seperate FOC, you can do whatever you want if you use two FOC, it doesnt matter if it has sub-humans, or aliens for that matter. you can take any two armies with two FOC, one for dark angels, or any other army, and one with whatever other army you want.
dark angels and eldar, or grey knights and khorne.
its possible, but stupid. why would GK and world eaters fight beside each other? not fluffy.
i take two FOC for my space marines, but its an inquisitorial detachment. all thats in it is an inquisitor, two SOB squads, and a dominion squad. the only reason i do it is because i want to split up 20 SOB into two seperate squads. i could, using one huge squad, have just one FOC. using two FOC, you can do whatever the heck you want, and alot of the time people do mass cheese lists. theres no restrictions in that area, you just need your opponents permission.