I frequently train "weak spots" in that I may emphasize walking on my hands for a month or more doing varying amounts of them before or after the WOD very much in accordance with Pavels' Grease the Groove principles. My "thing" is capoeira and this emphasis has paid off quite well.
Your friends anger is perhaps misguided in that on the surface Westsides Conjugate method is very cookie cutter and can look quite a bit like Crossfit (Max Effort press day, Speed squat/DL etc.) The weaknesses your friend mentions are only observed by a knowledgable coach (Louie Simons, Dave Tate) and a solution is prescribed. Crossfit is no different. The WOD is a starting point as are the areas of emphasis in the Conjugate Method of Westside. Both methodologies are based on sound principles and the bottom line is they deliver.
As to addressing your hamstring issue the WOD constantly trains the posterior chain (please read the Crossfit Journal covering the press, push press, push jerk...the concept of muted hip function is covered extensively) DL, Cleans, snatches, sprints, rowing, KB swings etc. The training stimulus is there as to whether the technique is there that is up to you. Finding a qualified coach or having the ability for excellent self analysis is key.
I hope this helps