I don't think there are many penalties in terms of Google if you're just using simple redirects to clean up the links and make them look "pretty" instead of lots of strange numbers and letters like most networks provide. In fact, from reading on forums and various discussions with affiliates I believe most do this in some form.
PHP and .htaccess seem to be the most common that I've seen employed, and PHP is really easy to do. I wrote a blog post a long while back about it:
PHP Affiliate Link Masking