No, I don't know a lot about programming, but considering that these people do this stuff for a living, and considering that the bonus characters didn't have a story anyway, it seems that anyone with a functioning movelist (like Kitana, Reptile, Cage, etc.) could've been tossed into the game without too much hassle. If it can be done by hackers via modded Xboxes and cheat devices and the like, then surely the people who programmed the game could've done it.
The only problem I really see with that would be adding the move upgrades that you gain from experience, but if these were simply "bonus" characters like Scorpion and Sub-Zero, they could probably even leave those out. The developers even said themselves that they could've either had many more playable characters with much fewer upgrades, or fewer characters with more upgrades.
Also, adding the two most popular characters in MK history to the lineup could only have helped sales. Realistically, only allowing people to play as either Kung Lao or Liu Kang would make the game too niche for a lot of people, especially those who aren't extremely hardcore MK fans. Even within the fanbase, you have a lot of different people with a lot of different tastes in characters, so it's only natural for the team to allow you to play as more than the main two. Yes, it's a Liu Kang/Kung Lao game, but it's a Mortal Kombat game first.