The other way is to use two clocks running at slightly different frequencies. You start one at the beginning pulse and one at the end pulse, then wait until the have a coincidence. This acts like a 'verneir scale' to measure the time difference more accurately.
but now, you have TWO clocks that add to the uncertainty, no? even if one is rock solid perfect, the other one may not be. seems you traded one variable for two, now (?)
would those 2 clocks be harmonically related or would you want them to be a non-multiple of the first one? if one is related to the other, then you could have one source creating 2 clock outputs, but I'm not sure that's helpful.
I like the idea of charging a cap and measuring it at the end of the interval. you have problems with that, to handle, though: accurate measurement, slight variation from the real 'freeze' time to the time you aquire the voltage and measure it. what I like about this is that there are no clocks; you simply start charging a cap at the start of the 1sec cycle and then immediately measure it at the end (or, if you want to use discharge instead of charge, do the opposite).
now, how repeatable will the charging of the cap be? the cap will show 'wear' over time and so, will this be precise enough long-term? the cap timing may vary as it goes from cold to warm. surrounding temperature will also cause data variation. psu has to be very clean and volt meter has to be very accurate and stable.