The security protocols, I can imagine, would be in place to protect the Omnitrix and its user.
The Omnitrix doesn't reconstruct Ben's body, but it prevents him from dying by changing him into a specific form to get around the circumstances of death. The way I see the protocols are like this:
Protocol 1 - Prevent User Death: In the case of the User dying, the Omnitrix will perform an analysis, and will automatically transform the User into the form deemed fit to either prevent death, or if death has already occurred, revive the User.
Protocol 2 - Prevent Outside Tampering/Removal With Brute Force: Should the Omnitrix unit itself come under enough strain, perhaps an attempt at removal, the Omnitrix will undergo a short energy surge, enough to release a shockwave that pushes back against whatever force is acting upon it.
Protocol 3 - Prevent Unwanted Possession of User: If the User is transformed, they will be surrounded by a low-level energy field which prevents possession by other life-forms. If the User is not transformed, but is still possessed, the Omnitrix will sample and/or absorb the possessor (depending on how the possession works) and transform the User into the same species.
So yeah, tl;dr, the Omnitrix doesn't want the user (Ben) to die, so has protocols in place to prevent or possibly reverse it.