The Falcon 9 ended up in a slightly different position/velocity than was expected, and the primary mission (deliver to the ISS and don't dare run anything into it) took complete priority over the secondary mission of launching the other satellite into a high orbit.
if there was not at least a 99 percent chance that the rocket had enough fuel to complete the burn
The problem was a (very small, almost surely overstated, but there nonetheless) risk to the ISS. From Orbcomm's press release: "the rocket did not comply with a preplanned International Space Station (ISS) safety gate to allow it to execute the second burn."
Goodwill in the space community and helping to defray costs of future launches by making commercial launches more successful (and thus less expensive, if only for insurance purposes) seem like things that benefit their operations. Perhaps this is a naive opinion, though.
Purely on the basis that the new trajectory can't be gone over with a pin, even if all the maths comes out saying that everything is lovely, you do not refire an ISS delivery rocket that is not where you expected it to be, especially one that has already sustained damage, just to test a new robot.
Here's to many, many more private space successes!