Yes. I think it is OK to do so.
Another good option would be to use an ad server. For example you may use openads.org (previously PHPadsnew).
Using an ad server, you can display ads as you wish. For example, you can change the color of the ad links for every impression and is can be beneficial as users won't get used to seeing the same ads again and again.
You may also use more than one network. For example: you can rotate adsense and YPN or clicksor and see whether it is beneficial or not. Of course you can also create your own ads with affiliate links in them.
To install Openads, you can use fantastico in cpanel. It is as easy as few clicks of the mouse. Try it and you won't be disappointed.