How to safely grill meat/fruit/veggie skewers
Honestly, while your typical "combination" skewer looks more impressive, I find it's much better to grill them in separate skewers.  One for beef, one for chicken, one for peppers, one for onions, etc.  That way, you can cook each to their preferred temperature and not have to worry about the exact problem you're running into.

As far as cross contamination, you'll definitely minimize any risk grilling them as separate skewers, but since you didn't have chicken in the mix you should be relatively safe anyway.  Once you sear the outside of the beef, you should be safe.

I picked this method up from an Alton Brown recommendation on a Good Eats episode (Scene 10), and found that I get considerably better results when I do it this way.