In no particular order:
1. Implement a screening or initial evaluation process each new member has to go through. Something is better than nothing. Gray Cook's FMS is getting a lot of press lately, and is easy to learn and implement.
1a. Alternative WODs for those with orthopedic issues, or with problems that the screen shows, or whom may be in special populations.
2. An intensive period of instruction on the basic "slow" lifts for strength AND other movements frequently used. I like Rippetoe's movements from SS, except I would sub the high bar squat for the low bar squat for assorted reasons I am not going to get into. The NorCal S&C "On Ramp" concept is going in the correct direction.
3. Eliminate all variants of cleans and snatches from all metcons. Implement an "Olympic Lifting Basics" class for those interested in it for the sake of training variety or competition.
4. Require a certain number of dead hang pull-ups to be a requirement for kipping pull-ups for non-Crossfit games participants. For Games competitors, proper instruction and programming for the kip and butterfly kip is essential.
5. Implement a standard warm-up and cool-down.
6. Eliminate the GHD sit-up.
7. Implement site-specific programming based on the needs of your client population. Despite protestations to the contrary, the WOD has been pretty much random since WOD #1. These were appropriate for the original group of Crossfitters, maybe, but not for your clientele.
8. Require professionalism from your trainers.