I like the S08SHx chips. As you've discovered, the architects have tried to offer a range of functionality but it can make you choose some feature over another. Some would say look at another chip but the S08SHx for some reason may be your only choice.
As has been mentioned recently in this forum, you could alternatively use the input capture timer channels and count edge interrupts. This would leave the pin free to use as reset. But it means for the timer input capture pin an interrupt occurs on every edge(up&down) or second edge(up or down).
The risk is if the frequency of your clocks/frequently transiting input is very high, maybe the interrupts can't be serviced fast enough or it hogs processing time for other routines.
If this was possible for your project, you could use the reset pin and still count edges of some signal.
Another option though unattractive, is to use some sort of supervisory circuit/IC with a reset input to cycle power to the uC. That would free the pin for TCLK and still have a RESET. A bit messy though.
John Dowdell