As others have suggested, Alma must have found the situation after Jack's arrival very confusing, maybe even threatening, especially when you consider how little she knows about this fella called Jack who has so suddenly entered her life. All she knows is that he has sent her husband a postcard, letting him know that he'll be passing through Riverton on a certain date and suggesting the two of them might get together for a beer. When she asks Ennis who this Jack is, he lies to her. He denies that they "coyboy'ed" together but were, instead, "fishing buddies". (Why this lie? Is Ennis quickly and cleverly establishing a cover story for a possibly prolonged visit from Jack?) However, when she briefly gets to meet Jack, one thing she learns about him is that he is a married man with a young child. This is, at least, something she can cling on to. He is a regular married guy with a young child, much like Ennis and herself.
So I think Alma's invitation for coffee is an attempt to get the world back into a normality she is comfortable with. Clearly, for Alma it's been a bizarre evening and night, with the kissing to start with and then Ennis not returning after they leave for their drinking session. Now Ennis is flying around their apartment, quickly together all he needs to go off on this fishing trip with his buddy.
Alma's invitation for coffee, then, is probably a desperate attempt to bring the world back to what it was like before Jack arrived. If she can only get Jack up to the apartment, then she can find out more about his wife, his young son, maybe even see some photos that many men carry in their wallets of their wife and children. The framework of her world would then at least have the outlines of the sort of world she is familiar with.
Of course, this doesn't happen. All Alma can do is to tearfully watch their departure, unsure of what world she now is in. It will take a long while for her to work that one out.