It is a risk to depend on a third-party (Apple, or even MacPorts) to keep your software stack up-to-date for PCI compliance. Learn how to compile the components yourself, and install them outside of where Apple does: this will protect you from poorly-written Software Updates (like the recent Apple Perl/CPAN update error) from damaging or reverting your installation. Disable Apple's Apache and MySQL and enable yours.
Review the builds at opensource.apple.com and www.macports.org for guidance. Block software you cannot/should not upgrade (such as Kerberos) using the operating system firewall and with a network firewall.
Consider:
cd /usr/local/src/
tar -xf mysql-5.0.83.tar
cd mysql-5.0.83
./configure --prefix=/usr/local/mysql --enable-local-infile --enable-shared --enable-thread-safe-client --with-extra-charsets=complex
make clean
make && make install
tar -xf httpd-2.2.11.tar
cd httpd-2.2.11
./configure --prefix=/usr/local/apache2 --enable-mods-shared=all
make clean
make && make install
tar -xf php-5.2.10.tar
cd php-5.2.10
./configure --prefix=/usr/local/php-x --enable-dbase --enable-ftp --enable-mbstring --enable-xml --enable-zip --with-apxs2=/usr/local/apache2/bin/apxs
...
/Library/LaunchDaemons/com.your.httpd.plist
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>EnvironmentVariables</key>
<dict>
<key>DYLD_LIBRARY_PATH</key>
<string>/usr/local/apache2/lib</string>
</dict>
<key>Label</key>
<string>com.you.httpd</string>
<key>OnDemand</key>
<false/>
<key>ProgramArguments</key>
<array>
<string>/usr/local/apache2/bin/httpd</string>
<string>-D</string>
<string>FOREGROUND</string>
</array>
</dict>
</plist>
/Library/LaunchDaemons/com.your.mysqld.plist
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
<dict>
<key>KeepAlive</key>
<true/>
<key>Label</key>
<string>com.your.mysqld</string>
<key>Program</key>
<string>/usr/local/mysql/bin/mysqld_safe</string>
<key>RunAtLoad</key>
<true/>
<key>UserName</key>
<string>_mysql</string>
<key>WorkingDirectory</key>
<string>/usr/local/mysql</string>
</dict>
</plist>