Peter, take a look at the High Speed Counter module for the GE Fanuc RX3i, part number IC695HSC304. The manual is GFK-2441, available from GE Fanuc's website.
I don't have time to delve deeply enough into the manual to give you a definitive answer to whether or not it can output a 2.5 kHz square wave pulse train, but it looks possible. The module has outputs that can be directly controlled by the counter's accumulated value, independent of the PLC scan. It can handle 1.5 mHz pulse rates and also has an internal oscillator that can be applied to the accumulator.
I'm more familiar with the High speed counter for the 90-30 platform, and I know the best you could get with that one was 2 kHz. The specs listed the output update rate at 500 microseconds. I could not find a similar statement in the manual for the IC695HSC304. However, the specs for everything in the RX3i module are better/faster than the corresponding parameter in the 90-30 module. The only spec I could find was the "Output delay time" on page 1-3 of the manual. Output delay from On to Off is listed at 125 microseconds and Off to On is 85 microseconds. In the chapter where they describe how to set up an output to respond to the accumulator value (pp 3-18 to 3-20), they mention that it is possible to set up an output range too fine to actually switch the output and refer to those output delay times.
Bottom line, since you're looking for an off-the-shelf, documented solution, this could do it for you. Worth a look.