A resistance only limit current, you need a voltage divider if you want to limit the voltage.
Also, high speed digital (everything above 20 MHz) don't like any such thing, such as voltage divider and other low cost / easy thinking way of voltage conversion. Those usually limit the transition speed of the signal, because of capacitance and inductance effect. Almost everything is a Mosfet... if you put a resistance, you also limit the gate charge and discharge time. There must be a better way to connect 5V PCI to Spartan 6... Doesn't PCI use LVDS interface ? There exist transceiver for that, and in fact, I never heard anything connected to PCI or PCIe without a transceiver. Some FPGA even got the transceiver, so no need for an external one.
EDIT: PCI doesn't use LVDS. It use 3.3 V signaling. Just use a voltage converter.
EDIT EIDT: PCI can either be 3.3V or 5V. Check your system to be sure. Also, you will need some bidirectional converter for some of the line.