The Glasgow winger decided to make the move south even though Northampton have had a poor season and are unlikely to qualify for the Heineken Cup.
The move further undermines the "fortress Scotland" plan devised by the national coach.
Glasgow's head coach Hugh Campbell told The Scotsman: "It is a big disappointment to lose Sean, but if his heart is set on moving then there is not much we can do.
"He has to think about the possibility that Saints will be relegated and the likelihood that they won't be figuring in next season's Heineken Cup. If he is happy at that prospect, then so be it."