Yeah, if we're being very technical, you're right. But the sample problems on that link asked to calculate the "disintegration energy" (which can be interpreted as a magnitude so really it doesn't matter whether it's positive or negative).

The formula Q = m_{final}c^{2} - m_{initial}c^{2} is okay with thermodynamics when calculating change in energy (which of course is always negative, exothermic, for decay reactions).

But once again, the questions on that link are pretty much asking "how much energy is released?" in which you would just reply with a magnitude, since negative is already implied.