I have a (B.Eng) degree in software engineering. I started out in the R&D startup world in 2003, doing the usual CS/SE things like QA, maintenance programming, and finally ending up in requirements analysis/system design. In 2007 I decided that I didn't want to spend my life working for stock options that aren't worth the paper they're printed on and went for a career change into IT. With zero helpdesk experience I interviewed for a senior Linux sysadmin position in the IT outsourcing branch of at a major (Fortune500) telco -- got a job offer the same day. Fast forward 5 years later I'm still with the same company but I'm now a sales engineer supporting salespeople that sell the same IT services I used to run. The kicker -- I make double the money that I did doing R&D.
I'd say that if you know your shit and can get shit done, then it doesn't matter if you're trying to do CS with IT experience (or vice versa). Good employers will even consider it an asset to have experience from "the other side of the fence". IMHO IT knowledge will make you a better programmer, and CS knowledge will make you a better sysadmin. You'd be surprised how many PHP/Java web developers don't understand the support consequences of their sloppy code -- they only see as far as QA. A PHP injection flaw on a web page that gets 10M+ views/day will generate a LOT of phone calls.