Every startup script is run by root which makes sense if you think about it.
Most of the daemons that do not need root privs su to a different user upon execution.
If your program needs root privs then there is no special changes.
Having said that, if your program does not read any data from users, then it is acceptable to let it run as root.
Put another way. if user "ausr" hacks the account "lusr" then any process owned by "luser" is at risk.
For those critical apps that run in a hostile environment, I lock the pi account, create a new one, assign a good passwd to root and use su, not sudo as needed. Put another way, sudo is a security risk as it requires no password. Might as well just log in as root and be done with it.
Doing Unix since 1985.
The 9-25-2013 image of Wheezy can be found at: