Afraid you're pretty much stuck using php.ini to disable most of those. However, it gets worse. eval() is technically not a function, it is a language construct, so it CANNOT be disabled using disable_functions. In order to do that, you would have to install something like Suhosin and disable it from there.
A good webmaster should consider a security review to be an essential part of site setup. Do not try to completely abstract this away, people are lazy enough about security already. If you are going to use tools (like a webhost), you should take the initiative to have at least a cursory knowledge of how to manage one responsibly.
That said, there are some other things you can do to severely cripple most hack attempts, including:
-Disable base64_decode() using disable_functions. Now, there are ways around this, however the vast majority of hack scripts are generic in nature, and this will break about 95% of them as they require the existence of BOTH of these functions in order to operate properly. This does not mean that your server cannot be hacked, but in most cases it would incur the overhead of manually sniffing your server for vulnerabilities, and most hackers are playing the numbers and ain't got time for that (NOTE: some hackers do have time for that, this is not a magic bullet by itself).
-Filter all input for common other exploit string patterns like <?php, which is frequently used to squeak by an opening php tag unnoticed. There are several such patterns. Best practice is to whitelist specific characters and reject all others on a per-input basis. At the very least, filter the aforementioned, null terminators, and possible sql injection strings such as '; -- (do not assume that simply using pdo or mysqli is going to filter ALL injection attempts, there are still some ways to pull this off even if you are properly using prepared statements).
-Any directories that serve only media should have all script access disabled, and all uploads and media should be placed only in such a directory. It is better to whitelist only the acceptable media rather than blacklist scripts, as there are any number of ways to execute a script file (eg: php, php5, phtml, etc) which individually may or may not be available on any given server environment. You can do this with a simple .htaccess placed in the media directory similar to this:
php_flag engine off
AddHandler cgi-script .php .php3 .php4 .phtml .pl .py .jsp .asp .aspx .htm .html .shtml .sh .cgi
Options -Indexes -ExecCGI
<Files ".(jpe?g|png|gif|bmp|tiff|swf|flv|mov|avi|mp4)$">
order deny,allow
deny from all
</Files>
This part can be dynamically written by php, so your application would be capable of securing sensitive directories in a manner similar to this, which can mitigate a great deal of hacker pain, as this is typically overlooked. I typically add a similar .htaccess to almost every Wordpress site I work on in the uploads directory, and have often wondered why this is not done out of the box, as it blocks a great deal of hack attempts and does not interfere with the application in any way that I have noticed.
Unfortunately, if you are not on an apache server, you will need to find another solution (on IIS there is most likely an equivalent, but I am not aware of what it would be personally).
-You should also configure your .htaccess (or web.config/etc) to disable any access methods that are not needed for your specific application. If you are not doing RESTful web services, there is really no reason to allow PUT or DELETE, you should almost certainly also disable TRACE, and probably also don't really have any reason to leave OPTIONS or HEAD enabled either. It should also be mentioned that all non-recognized connection methods by default resolve to GET, which means that from the command line I can do something like:
curl -X BOOGITY -d arg=badstuff -d arg2=morebadstuff yoursite.com
In this example, BOOGITY is meaningless, however, your server will interpret this as:
curl -X GET -d arg=badstuff -d arg2=morebadstuff yoursite.com
However your application likely will not.
In order to prevent this, you should configure your server to accept only GET as GET, and not allow it to be the default.
In most cases, the primary point is not to make it difficult to execute specific php patterns in your environment, the point is to prevent the inclusion of rogue code (either locally or externally) so it does not become an issue. If you are allowing the installation of modules or such into your CMS, sloppy programmers WILL eventually create exploits, which you cannot really do much about aside from enforcing pretty stringent API parameters that make it very difficult to do it poorly, but it can never be made impossible. Never underestimate the capacity of an offshore hack shop or self proclaimed "php ninja" to diligently work with your system in the most insecure or non-compliant way possible, create massive vulnerabilities, and to invent any number of roundabout hacks to do so that are actually harder to pull off than just doing it the right way.
/security rant.
