That is a good point, I understand the concept of non blocking code and unfortunately there are several portions that are. A lot of comments keep referring to the speed of the event, from reading the info on the Arduino site and a few others, it seems that both the speed and priority of the event are considered when deciding to use an interrupt. If you have several say, 100 sequential events and one additional event that requires priority, does it make sense to code all 100 "non blocking" just for the one high priority event to be timely captured or would it make more sense to just use an interrupt.
Several matters are involved.
Firstly as others have pointed out, "blocking" code is virtually certainly going to bite you sooner or later, so your priority needs to be to resolve that because the blocking code is going to affect events that you perhaps didn't think were needing such priority, but actually do. Alternatively, it is highly likely that having troublesome blocking code is going to make later additions to the code much more difficult - which is really what you are experiencing now.
If something is of significant priority, you make it a subroutine, and call it regularly interspersed within your 100 other functions. Particularly for what you describe, you are hardly likely to be concerned about execution time.
Secondly, there is a limit to what you can do in an interrupt. You cannot do anything that in itself, involves interrupts or takes some time, such as communication (via the serial interface, or I2C, or SPI) - because these involve or may affect the timer interrupts. I am betting that what you imagine doing in this interrupt does - or you would like it to - involve something like this. What you generally can do is to set something immediately, likely an output and/ or a "flag" variable which will later be processed by the main loop.
Finally, you need to be careful about what can happen when an interrupt occurs within the execution of another function - where such function involves the same hardware or software elements which the interrupt will use.