I'm pretty sure that was the main reason. All reports are that they offered Lehner a 2 year contract at the same 5 per year money that he signed for in Chicago for one year, and Lehner declined it wanting a longer term. Doesn't seem anyone else was willing to give him that term at that money either since he signed a one year deal, so it's not like Lou was alone in these concerns. I don't think the thought was so much that Varlamov was necessarily the better goalie, but more that he was the more reliable bet over a 4 year deal due to fears of Lehner relapsing, not to mention that having one of Sorokin's idols on the team would be good incentive to get him to sign here.
The other part about Lehner was that season really shown a spotlight on him. He was very out front about him. While he thanked the team and fans routinely, he was the storyline that season. Doesn’t seem like a Lou-approved storyline above the team. Lehner almost became a media distraction in A way taking away from the team. Seems to me like Lou made an offer, one the player was not expecting, Lou really wanted Varly, but kept the Lehner option open to upping the offer, if needed. He didn’t need it, Lehner hoped Isles would amend, market moved, Isles got their guy, Lehner had to scramble. You are a UFA - time to look out for yourself as a player in whatever way you want: money, term, team, location, teammates, etc.
Lehner is an excellent goalie, but didn’t seem to me to fit Lou’s team-first motto.