He has his own faction and temples though, and it is listed as the http://www.uesp.net/wiki/Lore:Ebonarm#Ebonarm.
Figures, gods of peace don't like competition.
Anyway, the end all is that Ebon Arm is too crude to fit in properly. Which is understandable, he is only a regional deity so he doesn't get a fresh coat of nuance with every game. Sure he can be made to fit but he'll lose 'status' compared to the Aedra and Daedra.
So my suggestion remains to see him as once a follower of Stendar. It is possible to relate these two opposite gods because the truth is always much more nuanced then it's descriptor card. Stendar is more then peace, he's more often called mercy or righteous rule. In his Nordic guise he's a warrior, a clever one that captures rather then kills.
We should be able to say the same about Ebon Arm, perhaps not so much a god of war as a god of soldiers and fighters. One they sacrifice too say that their enemies may have mercy and that they may life and this this how Ebon Arm showed himself in his only myth.
How he became divine, I'm afraid we'll never know. Perhaps he once realized that it is better to be merciful then to hope to receive it. Perhaps he once realized that only through war one could accomplish peace. Or perhaps, he was a merely a hero dedicated to Stendar that once wandered up to a battle field, heard the arguments from both sides and in doing so they realized their mutual stupidity. Once witnessed by thousands his name would be whispered by millions in prayer and there he was.