Lineen has been part of the Glasgow coaching staff for nine years but will continue to play a role for the Warriors as he takes on the role of head of acquisition at Scottish Rugby as well as coaching Scotland U20's.
The 50-year-old will be replaced at Glasgow by Gregor Townsend, the current Scotland assistant coach, who will end his work with Andy Robinson at the end of the Six Nations.
And while admitting his surprise at the timing of Lineen's departure, Nicol has called on Glasgow to ensure they send the New Zealander out in style.
"Sean is an outstanding individual as well as a coach, He'll make sure their heads are right," he said.
"If Sean is leaving the players should send him out with something to be really proud of.
"There will be a job to do to get the players back on line (but) they will just knuckle down.
"Glasgow have become a very hard team to beat. It's all a bit surprising.
"It's not surprising that Gregor Townsend is getting more coaching but just the manner, the timing of it."
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