Wouldn't this lead to more Liberal opposition to Chretien and perhaps lead to an early resignation and PM Martin?
Nah. Unlike Australia where a leader can be toppled on an hour's notice (or UK, closer to Canada but not as extreme) Canadian leaders are basically invulnerable to the whims of their party for long stretches of time. There's a reason it is called the Elected Dictatorship sometimes.
As long as Chretien has the confidence of the House (which he will, one way or another, given the opposition of the time) he will be fine. Now if he wins another minority in 2000-2002 then he'll have problems, because Paul Martin might have the balls to stab him in the front. But he'll likely win a majority, and perhaps even crush Martin.
Very different Liberal Party circa 2005-8 though, potentially, plus major butterflies on how or if the right wing gets it together.