Ultimately that's what you have to do - you've got two different code paths, so there needs to be an if or function pointer in there somewhere to distinguish. As patio11 mentions, you can hide that with Strategy patterns, closures, frameworks, etc, but I'm not sure it buys you anything. You'd still need to retrofit your code to use those patterns, which may be more invasive than just using an if-statement. (Particularly since you want to remove the code if the experiment doesn't pan out, to avoid bloat.)

Another option is to branch your codebase and then proxy requests through to a new appserver running on the branch. This keeps the individual codebases simple, but merges suck - and if you don't stop development entirely, you'll need to be merging several times over the length of the experiment. (Also, this is one way experiments go wrong - a change to an unrelated feature can often have unexpected results on your data.) It's also a deployment pain if you're just a startup with a couple developers.