Almost certainly not. It's possible that under the new rules allowing freeware, certain custom levels, custom campaigns and total conversion mods of some games will be allowed, but I can't see SDA ever allowing the original campaign of a game to be run with mods installed.
Except for Half-Life.
Well, technically no. Except for all the games have been allowed to use mods under the established convention that modding strictly for the purpose of introducing a timer or demo recording is usually allowed. Half Life is slightly different to the rest in that rather than using a mod that adds in demo recording (or in this specific case, make demo recording actually usuable), they use an official patch to fix the demo recording and then use a mod to undo all the gameplay effects of that patch, thus producing the same effect as playing on a previous version with demo recording modded in.
There certainly
is a significant difference between this and simply modding the demo recording into the older version, especially since someone could reasonably raise the question of how we know that the patch didn't have some gameplay effect we don't know about besides the bunny hopping capping that the mods undo; clearly an undetected change made by an official patch - which could do pretty much anything - is more likely than an unintended change made by a mod whose sole purpose is to add in demo recording or a timer. However, the Half Life mod use is nowhere near the huge issue people make it out to be, and is only a small deviation from what SDA accepts in other games.