Using other oscillators on the altera demo boards is not only possible, but in some cases even neccessary. In my case, I had to generate a clock frequency of 52428800 Hz to synchronize to external events with a given precision. This is impossible to do with a PLL fed by 50 MHz. So I changed the onboard oscillator to one with a frequency of 32.768 MHz, set the PLL multiplier to 8/5 and got the desired output frequency.
The only thing you have to be aware of, is that the altera boards (in my case the NIOS Stratix Dev. Kit) demand an oscillator running at a voltage of 5V. If your oscillator is a 3 Volt type, you need some glue parts. Contact your hardware guy to help you out, if you don't know what i mean...
Klaus