Is it unwise to start a Ms/PhD program without a stipend - will it upset professors if I leave with a masters to apply to funded programs? I was recently notified that I was accepted to a Ms/PhD program with a full tuition scholarship but I am waitlisted for receiving a Stipend. I don't currently have the best credentials so I don't think the prospect of me getting into a better program is too good. 

Would it be unwise for me to start this program? For now my plan is to attend until I get an MS and then at that point apply to a better program if I still don't have a stipend. I figure a tuition free MS is better than the usual.

By "unwise" I meant, will it potentially upset professors if I leave after two years with the masters to apply elsewhere to potentially funded programs (if I still don't have a stipend at that point). I don't want to ruin my reputation in the process.
I think that you are more asking, whether it is common to start graduate school without funding. Generally at the MS level, it is not uncommon for MS students to be unfunded. All depends on the school. Most schools that I've encountered would much rather fund PhD students since you get more out of the students.

Now at the PhD level - I would not advise a PhD without funding. Trying to live 4-6 years without a salary is difficult, and most people I've seen try this failed. There are enough schools out there that you should be able to get funding somewhere (unless you really have bad scores/grades and shouldn't be in graduate school).