The problem is, we're dealing with a tech that operates similar to, but differently, to us.
We have never fought an enemy that could over-ride our computer programmes, ordering our weapons to open fire on our own side, or opening us into space.
The Colonials fought the Cylons for over a decade, and it stands to reason that their computer-systems are designed resistant to Cylon interference. We just haven't had someone sit down for a episode explaining how different their computer systems are to ours. DRADIS would appear to be the weak-link, as it has
to accept incoming data or it would not work, but shutting off DRADIS, while giving the Cylons an advantage, would not be as devastating as taking power or weapons off-line. From the experiences of the Pegasus
in Razor it would seem that weapon stations have their own individual control so could continue firing on manual, even without DRADIS, as engagement appears to be mainly at visual range anyway.
The Colonials were going back to a wholly-networked system, hence the CNP back-door that enabled the Cylon Virus and Logic Bombs to swiftly move from system-system. The CNP could even over-ride any normal virus-warnings that they have (in the Mini Starbuck's Viper systems appeared to give some kind of warning of an incoming virus).
s computers may be arranged, they are resistant to the virus infiltration, as evidenced in the Mini. But, as I said, no-one's sat down to explain why.