Shedon:

Похоже мы вас в заблуждение ввели. В мануале четко написано, что вход Capture можно использовать как счетный, если выставить нужные биты в TxCTCR.
Count Control Register (CTCR: TIMER0 - T0CTCR: 0xE0004070; TIMER1 - T1TCR: 0xE0008070)
The Count Control Register (CTCR) is used to select between Timer and Counter mode, and in Counter mode to select the pin
and edge(s) for counting.
When Counter Mode is chosen as a mode of operation, the CAP input (selected by the CTCR bits 3:2) is sampled on every rising
edge of the pclk clock. After comparing two consecutive samples of this CAP input, one of the following four events is recognized:
rising edge, falling edge, either of edges or no changes in the level of the selected CAP input. Only if the identified event
corresponds to the one selected by bits 1:0 in the CTCR register, the Timer Counter register will be incremented.
Effective processing of the externaly supplied clock to the counter has some limitations. Since two successive rising edges of the
pclk clock are used to identify only one edge on the CAP selected input, the frequency of the CAP input can not exceed one half
of the pclk clock. Consequently, duration of the high/low levels on the same CAP input in this case can not be shorter than 1/fpclk.
Это значит что максимальная частота счета на практике будет чуть меньше PCLK/2, в вашем случае - примерно 28 МГц, и вы можете сделать нормальный частотомер.
Так что заботиться о прерываниях не стоит.