This weekend we grilled kebabs with steak, onions, peppers, and big pineapple spears. No ill effects, but I noticed that the pineapple was still cool where it was touching the meat, and the meat still reddish where touching the pineapple. This made me wonder whether having the chunks all snugged up against each other is truly safe or not, it seems like any bacteria on either piece would still be safely alive and dangerous where they were touching. Any good knowledge on this, or recommended practices for grilling safely?
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.