Hi Jabuti,
I guess the answer to your question is, not surprisingly, it depends. Many of the answers here are just spewed out based on some availability heuristics, but I can tell you tell that uneducated people speak any and every language poorly. That's just a fact.
Some things to consider:
I guess you're going to Cusco over "our Summer," which is "their Winter." It can get pretty chilly there - more so at night. Also, a significant percentage of their population speaks Quechua and other native languages which may confuse you a bit if you're seeking a pure Spanish learning experience. By way of reference, I spent my whole Summer of last year down in South America and it took me a while to get adjusted to the regional differences in the way Spanish is spoken. For the most part, it took me a bit to understand other people when they were talking among themselves. And I'm a native Spanish speaker!
On the other hand, Cusco is out of this world beautiful! A small town with the nicest people I've come across (tied with or a close second to Thai people) and the food is delicious, in my opinion.
Santiago is similar to Cusco in that it's the second biggest city in the country, but it's probably three times more densely populated. It has more of "city feel" to it. I've heard great things about the immersion program at PUCMM and it was a popular choice for some of my friends in Undergrad. I was always very impressed with how much they learned in a very short period of time. Further, the Spanish spoken is very neutral and transferable to any setting for sure.
I would venture to guess that the main concern is that you'll get some of the Cibao "i" for "r" substitution handicap, but I don't think that's a valid concern. At your level, you will be acquiring some vocabulary and grammar and will work on accent as you become more fluent. In essence, the environment where you practice your Spanish after the program will be more of a strong determinant of your accent than where you go for an initial introduction to the language.
Hope that helps,
Cris