Not sure I understand this. Isn't uploading your code to an AWS box "putting your IP on another company's servers"?
Unless you host your own email, servers, chat, storage and backups, you are putting your IP on another company's servers.
But if you do want to use Amazon securely I believe that they have the ability to encrypt your drive.
That said, rack space is incredibly cheap these days, and throwing in a 1u ubuntu server in a 1/4 secure rack is cheaper than hosting a dedicated vps at amazon.
I completly understand starting out using shared services as a startup, but eventually, and soon, you'll want to move to your own systems. It's just an expense for your business, and you would be irresponsible to leave your systems vulnerable.
(my projects have been more sensitive in the past than the typical CRUD app, and so perhaps I'm paranoid)
Moving to our systems only makes sense to me if its a core part of my business or if 3rd party solutions are inadequate. Paying 2 engineers $75/hr to reinvent IRC/git/email poorly is a poor use of time and money.
At the end of the day, if GitHub steals my IP (for whatever reason) I can sue GitHub (if its not morally wrong, they have a legal reason to discourage them from doing so). If my "1u ubuntu server" is hacked due to a poor default, I have no recourse.