You can generally mark if you'd like to be considered for MD-only admission on your secondary application. Most schools allow this, and some will automatically consider you, but there's a few that don't, and some have a convoluted process (for example, at UT Southwestern to be considered for MD-only you need to also fill out the TMDAS, but for only MD/PhD you just submit AMCAS).
Personally though, I feel like if you would be ok with MD only, you'd want to consider if the MD/PhD is really right for you. If you do plan to do basic research with just an MD (and you certainly can), then go right ahead, just know you'll need some strong research training after your residency. If instead you feel you want to do more translational research or would be happy with no research, the MD is probably better suited to your goals. Not everyone will agree with this, but just my 2 cents.