imho conflicts should be handled by marking packages as Conflicts and Obsoletes
in rpm:

Conflicts below:
php-pdo <---> php-pecl-pdo-sqlite
php-pdo <---> php-pecl-pdo
php-devel <---> php-pecl-pdo-devel

        file /etc/php.d/pdo_sqlite.ini from install of php-pdo-5.1.2-4.3
conflicts with file from package php-pecl-pdo-sqlite-0.3-3.fc5
        file /usr/lib64/php/modules/pdo_sqlite.so from install of
php-pdo-5.1.2-4.3 conflicts with file from package php-pecl-pdo-sqlite-0.3-3.fc5
        file /etc/php.d/pdo.ini from install of php-pdo-5.1.2-4.3 conflicts with
file from package php-pecl-pdo-1.0.2-1.fc5
        file /usr/lib64/php/modules/pdo.so from install of php-pdo-5.1.2-4.3
conflicts with file from package php-pecl-pdo-1.0.2-1.fc5
        file /usr/include/php/ext/pdo/php_pdo.h from install of
php-devel-5.1.2-4.3 conflicts with file from package php-pecl-pdo-devel-1.0.2-1.fc5
        file /usr/include/php/ext/pdo/php_pdo_driver.h from install of
php-devel-5.1.2-4.3 conflicts with file from package php-pecl-pdo-devel-1.0.2-1.fc5