Perhaps this was an attempt at a clever word play. He is separating himself from the company and used the word 'comma' either because of the frequency it appears with 'separated', or your colleague may have also intended 'comma' to be interpreted by one of its other meanings. Particularly, it may have been intended to mean 'a short pause' between two important objects--especially if your colleague was there for only a short period of time.
I suspect that it's probably the former, though, that he was announcing his separating from the company and threw in the 'comma' just because of its familiarity with 'separated'.
I long to see my wife, but for now... we're comma separated.– JCooper Mar 25 '11 at 15:51