[SSJKarma]

a program is a still a program, sentinel, like all computers can delete those programs. the only thing is... normally its a human who should do this manually, but sentinel has the power because it has an AI made for the purpose of being able to self protect and see what situation is best to achieve its goal !

so if the situation changes and brainiacs get in, sentinel willl just delete the new illegal program so it doesn't get in its main core ! not saying that its gonna work tho, but it sure won't be as easy as you say it will !

the sentinel can could self destruct itself if it sees no other choices, but its only a last time ressort. its not like sentinel would be as intelligent as to know that brainiacs is a all time villain that can take over computers, nor can it really decide his path in life. but it sure is intelligent enought to fight and know when its programming his in danger which it has been programmed to defend against !

that's why sentinels are known as MUTANT ASSASSIN, because they are hard as hell to kill !
that's also why after that master mold was destroyed, the government decided to keep the project but not as a giant size state like the original was. that's why we don't see much of sentinels in the series after master mold's destruction !