I propose building security be tied directly to your SIC encryption keys and biometrics that can be exploitable. In the case of SIC encryption keys, having a recent one used in the last 45 days should permit access to certain door security. Additionally, retinal scanners should be able to be exploited via fancy cybernetic eyes used by deckers or the still intact eyeball of a donor.
Beyond this, this level of breaking and entering should be limited to gold sector and PC employed buildings.
Beyond a security refactor code-wise, all the specific corporate assets in these buildings will also need to be looked at to account for malicious IC intent, but this would be a huge step in intrigue and aggressive action that is empowered solely in the players hands.