Hmm, to be honest I can't think of an easy way to re-add the atmosphere with OPM. If you go into GameData/XPC/PlanetConfigs/EelooAlt, open the Eeloo.cfg file and get rid of :NEEDS[!OPM] at the top it might re-add the atmosphere without messing up Eeloo's place around Sarnus, but it also might not.
In any case, the next time I update the mod I can make probably make it so that Eeloo keeps it's atmosphere even around Sarnus. It's just that OPM doesn't just move Eeloo, it also changes its surface. I'll have to think about what the best way to handle it.