Christopher: As you may be aware, there are several different types of esotropia; many of which can be corrected through corrective glasses, surgery or vision therapy. As for diplopia, many of the same treatments are available. If either of these conditions are persistent and severe (ie, you haven't had them successfully, permanently corrected), then they will likely bar your entry to the CF. If they're corrected, or being managed, then you may have a shot, but will probably have a hard time getting into certain trades like combat arms.
In any case, speak to your doctor about the full extent of your condition, get as much documentation about your case, treatments, surgeries etc. and take all of that to see the recruiter. The more information you have prepared, the less running around you'll have to do later.