Yes. Manually using a heat gun (even a temperature controlled one) is a risky operation. The pins of an IC are designed to dissipate heat to the PCB so it is quite possible to have one side of your chip below the thermal failure tolerance while the other side is above that threshold, leading to potential damage to the silicon substrate in an isolated area.
Sounds like you got lucky in that you can see the damage straight-away rather than having an intermittent failure that might have only become apparent in the field.
There are products out there that make manual desoldering easier by dropping the melting point of your solder by forming a new alloy during desoldering. One such is ChipQuik but I have never used it myself for large chips. This makes it possible to melt all the solder simultaneously at a much lower temperature than normal (temps as low as 90 Celcius are possible, which is not likely to damage any IC I can think of).
(I don't work for the ChipQuik company by the way :))