running MRTG as root would be lame. some systems don't allow suid scripts. somewhere along the line you'll need an external progam (to suid root) to run the ping, might as well be ping.

if you're monitoring a lot of hosts, check if your router (or another of your SNMP agents) supports RFC 2925 Ping MIB. then you can request that the agent ping for you (and even send traps on failure) and collect the results from regular SNMP queries.