Just two points of clarification on this:
1) There's some disagreement in reporting on if Kaepernick or the 49ers are paying for the premiums on the insurance policy. The first report I read said Kaepernick is paying for it, which is also what Rapoport is saying. If Kaepernick is paying for the premium the 7.5 million pay-out is tax free (functionally equaling the 14.5 million injury guarantee he had, which would be taxed), which is why he would be the one paying for it, as if the team pays for it then the pay-out gets taxed and Kaepernick only ends up seeing about 8.5 of that 14.5.
2) If the team is paying for it, regardless of if it pays out or not the premium for it (said to be about 300K) goes against the 9ers salary cap next year, as it is in effect money being paid to Kaepernick in his new deal under the CBA.
My ASSUMPTION from #1 and #2 would be that Kaepernick is paying for it, and that the 1 million boost in his salary this year is effectively a way for the 9ers to indirectly pay for the premium which allows 1) Kaepernick to be the one paying for it so it doesn't get taxed on his end if he needs it and 2) the money going on this year's cap for the 9ers instead of next years cap.
I don't really see any upside for either party for the 9ers to be paying for it; both sides would be much better off (and Kaepernick's side in particular) if the 9ers just gave him the premium cost in increased salary this year.