From what I can tell, mod_php is really less secure in some ways than FastCGI (or SuPHP, for that matter) , thought it's (partly) a question of configuration and environment:
Main issue is apparently that mod_php runs as the Apache user (in Ubuntu that would typically be www-data), which means that you'll have to give this user r/w access to various files and folders on the disk. Some articles make this sound worse than it really is, though; you most definitely don't need to give it full access to all your files. Still, this can be a problem, especially in shared hosting environments. Also, unless you set up separate Apaches for each hosted site, if one of those sites has (critical) security issues, it could potentially compromise all other sites too.
To answer your question: when you're in control of the whole server and can set up permissions as you wish, I don't see this as a huge problem -- or, rather, I see it as a reasonable compromise. PHP as a module happens to be extremely fast, especially compared to something like CGI. You do want to be careful about what you install and run (and how you setup permissions on your server), but on the other hand, that's common sense anyway.
FastCGI needs more memory than mod_php, but provides more security too. CGI is by default both insecure and slow, but can be configured to be somewhat more secure. SuPHP is somewhere in the middle, more secure than mod_php but also slower than FastCGI or mod_php (though SuPHP memory consumption seems reasonable; this seems to be something of a problem for FastCGI).
Looks like your best bet would be either FastCGI (for security) or mod_php (for speed); latter requires care when setting up your environment, while former will apparently be slower no matter what you do. Decisions, decisions
(Note: I'm not an expert on any of this. I've always used mod_php for various reasons, and am pretty much used to any insecurities it brings about. Right now I'm looking into FastCGI myself, and I know that others have made PW run with it, but this isn't very high on my list to be honest.)