Perhaps a bit late, but overall, I feel that the two series are indeed in seperate universes. References aside, the differences are stark.
-In Halo, the UEG has governed humanity, the UNSC being its military and scientific arm. In Marathon, the United Earth Space Council (UESC) has governed humanity.
-The UESC Marathon was launched in 2472 and arrived at Tau Ceti in 2773. This is the first extro-solar UESC colony. In contrast, FTL travel in Halo had been developed by 2291, colonization beginning in 2362. Suffice to say, the ability to travel is stark.
-The Cyborg was among those who departed in the Marathon in 2472. In Halo, John was born in 2511.
There are probably more differences, but these are the ones I am aware of. Suffice to say, I can't see the two series being in the same universe. Rather, it's a case of in-game referencing, which is a common practice among game series.