In the rules, it states for 3 players, each player controls 2 teams, which means 12 terminators total. That in turn starts the scenario with the 12 terminator starting room and genestealer blips. However, if each player controls only 1 team, then it'll be 6 terminators, which is the same as a 1-player game. It should work, shouldn't it? Both games have 6 terminators.

obviously, it should work, and it will work.

the only thing that matter is to prepare the game according to the number of space marines, not to the number of player.

you can even play alone with all six teams in the game if you want ..., or in a two players game with 3 teams per player, as long as the choosen starting room feats the number of Terminators.