I think that's allowed.
What might not be allowed is substituting SAV for BOS.
Look up DL's Contract of Carriage:
Back to Back Ticketing - The issuance, purchase or usage of flight coupons from two or
more tickets issued at round trip fares, or the combination of two or more round trip
fares end to end on the same ticket for the purpose of circumventing minimum stay
requirements.
It doesn't look like you are circumventing minimum stay requirements.. I think the travel agency misunderstood the rule.
I have also done what you are describing many times and have never had a problem.