Nothing in the hints actually implies Momo scares him away.
Shanks W incoming.
OPTION 1: Aramaki is running away from Momo ---> That's ridicolous, not considering it as a real option.
OPTION 2: Aramaki is running away from Shanks ---> Unlikely, Shanks is already sailing away. What was the point of Shanks words last chapter?
OPTION 3: Aramaki is running away from the Alliance that came to assist Momo ---> That's more than acceptable. Only extreme Admiral fans think he has a chance against the Alliance.
OPTION 4: He's not really running away yet...?