For what it's worth: this is part of why I am still using the application version of Quicken rather than the online version. I want my data (and passwords) stored locally rather than on someone else's server where they are directly vulnerable to a data breach.
However, I do allow the desktop app to automatically download from (but not submit transactions to) my banks. The protection varies from bank to bank. Some required two-factor authentication every time, and Quicken correctly pauses for me to provide that. Others appear to negotiate a download - only password the first time Quicken connects to them, asking for the 2FA at that time and not needing it thereafter.
There is a newer, more secure banking protocol. Not all banks support it yet, and Quicken seems determined not to use it because it threatens their proprietary system. As soon as my banks do support that alternative, I will dump Quicken and move to an application using that.
There is some risk if the Quicken program itself picks up malicious code, but no more than if the bank gets hacked. Either way, you contact your bank and tell them the transaction was unauthorized, they and the target bank reverse the transaction, and the target account"s holder has to answer hard questions about what was going on. In other words, it is exactly as if someone had forged a check; the banking system knows what to do about this. It may be an unmitigated nuisance and a short-term disruption of your finances, but shouldn't be worse than that.
Note that the nonstandard payment methods used in scams (bitcoin, Western Union, and so on) are specifically employed to break that chain of accountability so the transaction cannot be reversed.