That's pretty much what I do. Even when making our favorite souvlaki, I usually make...
...skewers with just meat and skewers with just onion and bell pepper.
I double the marinade and marinate the meat and onions and peppers in one bag, and then a second bag of just onions and peppers. When I go to grill it, I only use the onions and peppers from the bag without the meat. I throw out the veggies that marinated with the meat, or cook them down in a large heavy skillet and use them for a condiment on grilled sausages, etc. I cook them really well, so no chance of bacterial contamination from the meat.
Michael