Two concerns with using plugs (one with sand, one without).
Concern one, no sand, just air: The air would want to expand considerably if it heats up and would increase internal pressure and might pop off of a plug (and all the problems that would cause) or just burst through the weakened tubing (bigger problem, lol). Considering how poor of a thermal conductor tubing is and how brief the exposure to the boiling water is, that might not be an issue though.
Concern two, using sand to occupy the space: the weakened/softened tubing might take the form of sand (especially if the grains are large) and would create bumps on the interior walls--leading to significantly increased turbulence (and therefore a likely increase in restriction). Yeah, it would take tubing from "non-factor" to "minimal factor" in overall loop flowrates, but still
Filling the entire tube with water and sealing the ends might be the way to go
Or use extremely fine grained sand
EDIT: Concern three: it wouldn't be very easy to do a long length of tubing, would it? You might need to coil it tight enough so it can fit in the pot and contain it with string or something that wouldn't interfere with the dye (and then remove the string upon removal so it doesn't leave an indent on the softened tubing).