I don't know IFMIS but from the little I gather, it sounds like a joke. You almost want to flag and prevent transactions happening at certain speeds. Perhaps buy time to alert an extra independent level of oversight(though we know these would be gamed without a question). That delay could save some money, because in Kenya, once the money is gone, it's gone.
"Flag" suggests notifying some person with the authority to look into the intended transactions and stop them if necessary. The problem here is that it is the "persons with authority" who are orchestrating the mischief. Also, delay is the last thing they want: approved in a day, into the bank, immediately withdrawn into a gunia is how it goes.
I am not a fan of technology solving what are essentially issues of character. But even with that in mind, this technology could still use some serious upgrade - that delay being merely part of it. It won't solve the problem, but it ought to be way harder to abuse the system. The system described by Kisero sounds like...it should never have been adopted to begin with.
Part of that upgrade could just be a simple requirement for more eyes...get more institutions or a requirement for a diverse group to look at certain types of transactions. When you have that, it's not impossible but just that little harder to steal. When you are stealing you don't want too many people in the loop.
If you watched Mangiti yesterday, he seems to suggest that the precursor to the looting was Waiguru putting "her" people in the correct positions. Mangiti was sidelined being a stranger. So you want to have a system that requires more strangers to look at and approve before anything is released. Again, I note technology while properly applied can add hoops, it will not solve the fundamental problem.