Unless you have very long beams I don't think it will make much of a difference. The axial load that gets into a moment frame beam is typically very small. These beams, in my experience anyway, are typically governed by controlling lateral drift. That, along with the fact that there are typically a lot of moment frames in a building, means each one takes not a whole lot of load. It also makes sense when you think about the fact that the moment frame members are really working in bending. I'm not sure how you typically model moment frames - if it's a single frame ( two columns and a beam) I put the windward a leeward forces at their actual respective locations. If you do this, you'll find the axial load is een smaller (and will actually probably be tension). If your software calcs the lateral loads for you and assigns their location in the diaphragm (as RAM SS does) then you'll have to pick a node to disconnect or you'll get no axial force) - this is the most conservative approach, and will result in the highest compressive (or tension) force.
To address the OP, though, I don't think a joist connected to the top flange only braces the beam against compression. More importantly, it doesn't brace it for negative bending and that will be more of a problem than the axial bracing.