It was ironic. She does find Scully inordinately hot, though...
She doesn't count herself as a shipper - she knew they were bound to get together, and that they
should get together, but they shouldn't have done it during the series, 'cause that's when it all went to poop. She also hated the super-soldiers more than life. And what was the whole Mulder-Jesus thing about? And Scully's Jesus-baby? AAAARGH!