Tiberium crystals are not individually all that strong- they are comparable to glass. Remember that Tiberium Harvesters are fairly simple in design- mechanical arms and cutters shear off crystals at ground level and scoop them into a storage tank (an early cutscene in TD shows a harvester driving over crystals, sending bits flying all over the place, accompanied by audible crunching sounds). There is no way that such crystals could withstand any of the punishment they took in-game; their apparent durability is therefore a gameplay decision rather than one based on the properties of the substance according to the story.

Short version: if a disrupter tank can shatter the heavy, multi-layered armors on the various combat units and base structures, it would damn well be able to shatter Tiberium crystals.

However, the disrupter weapon was a tightly focused beam which made contact only with anything in between the emitter and the intended target. It would not have affected anything at ground level right in front of the tank (there is an image somewhere of the tank firing its weapon; the visible distortion is clearly in the form of a beam several meters above ground level- were it not so, the tank would probably destroy itself right along with its target). As for why prone infantry right in front of the tank would take damage, the answer is as simple as the game engine- the game only supports one "level" for ground level. It has to treat a unit lying down or deployed the same way it would treat one undeployed or standing up. The only way around that would be to make the projectile ignore everything between the tank and the target point.