"Wrestle With It And Make It Your Own"
Litvak commenting on "Torah Is A Smorgasbord" :
R. Yaakov has given good advice.
Also, it should be noted that many other seforim today have portions of Gemara contained in them.
Let's say you are learning the Torah commentary of the Netziv, for example, which we discussed here recently. It is full of references to Gemaras and other teachings of Chazal (so much so that a beginner probably would be hard-pressed to follow them).
Could one say that learning it is totally 'leaving out' Gemara? I don't think so.
That is somewhat of an extreme example perhaps, but there are other such works as well.
Just as Tosfos (Rabbeinu Tam I think it was) famously stated that Talmud Bavli is a mixture of different parts of Torah, therefore one could fulfill the requirement of studying Chumash through it, so too, perhaps we can say that learning Chumash with a commentary that incorporates Gemara can fulfill the requirement to study Gemara!
Additionally, we must understand what 'Gemara' really means. Gemara is discussions of Torah, using the Mishna as a starting point. It is analysis and arguments of 'static' texts such as Mishna and Breisos, which make them come alive. When we treat Gemara as if it is a static text itself we are making it into a new, another layer of Mishna to a degree. But it's not meant to be like that. The correct idea is to take what you are learning, wrestle with it and make it your own.