Runtime reconfigurable FPGA clock routing
Dividing clocks locally is probably going to be the most straightfoward solution.  A major advantage is that the whole design will sit in one clock domain, so you don't have to worry about clock domain crossing.
Another option to consider for generating clock enables: instead of using a simple frequency divider, use a DDS-style accumulator.  This provides much finer frequency resolution, at the expense of a clock cycle of jitter.  But the jitter should not be a major issue if the system clock frequency is high enough.  This provides much finer control vs. a simple divider at lower division factors.  IMHO, this is probably the most straightforward and most flexible solution.
However, there are some other options to consider if you really want to use separate clocks.  At least on Xilinx devices, you have BUFGMUX primitives that can be used to select between two input clocks.  So what you could do is have, say, one &quot;standard&quot; clock that is provided to all channels, and one or more reconfigurable clocks that can be provided to small groups of channels.  Most likely you would want to use a separate PLL to generate these other clocks so you can also change the VCO frequency if needed.  In this way, you will have some additional flexibility, although unfortunately not complete flexibility as you only have 2 clock routing options for each channel.  There are also a limited number of BUFGMUX sites available.