Surely Eclipse is a DPS increase regardless of if you pay attention to the internal CD? As long as you swap to the other spell once it procs, you'll see a DPS increase, although not as much as if you use it "properly" and make sure you always proc the correct version of it.
Rawr.Moonkin does not model proccing the "correct" version; that is to say, when you proc Eclipse, you switch from Starfire to Wrath for the duration and then switch back. It is definitely a DPS increase if you do this. I may consider adding an option later to attempt to model proccing the "correct" Eclipse buff, but for now, consider Rawr's numbers on Eclipse a conservative estimate.
 Some further discoveries: I was incorrect in my conclusion that MF/SFx3/WxN was not viable at 80. It isn't viable at 80 _in level 70 gear_. After loading up a decent T7-level set, the Starfire glyph comes out as a DPS upgrade for both rotations. MF/SFx3/WxN is a clear winner at this gear level, also; I'm leaning toward the jump in spell hit and the almost absurd levels of crit and haste as factors. IS seems to be worth casting in almost every situation, save one: You're using Starfire as a main nuke (as under heavy amounts of haste), you have the SF and MF glyphs but no IS glyph. Lastly, it appears that spamming Wrath and switching to Starfire on an Eclipse proc may actually _not_ be higher DPS, as I indicated earlier. It appears to be situational. I haven't yet implemented the switch in Rawr that allows you to choose "smart" Eclipse procs.