Yes and no - while you won't be able to purchase marines at the beginning of a new game, picking one of the four 'Strategy' starting researches will re-enable recruiting them, but that locks out most of the Guard-specific content. The idea is that you choose to play as either the IG or the Ultramarines (with some minor guard support), and the new content this mod provides is balanced for not being able to use marines. For example, one of the first craft you get when picking the Guard over the marines holds 24 soldiers and has turrets, something that would be terribly overpowered that early in the game if those were 24 marines instead.