If you containerize, the application (malware) will run under the user configured in the image, unless you override it, and in a separate mount namespace, unless you change that, which makes the "alias sudo" trick extremely unlikely.

Even running under a separate user anyway prevents almost fully the attack you mention, unless the separate user has root privileges or the DAC_OVERRIDE capability is assigned to the binary (assigning it requires CAP_SYS_ADMIN).

In short, the attack you mention is a common persistence and privilege escalation vector, which is relatively easy to detect (watch for changes to shell profiles), although preventing it requires some care. I just want to point out that in single-user machines (e.g. personal computers) escalating to root is anyway fairly unnecessary, given that all the juicy stuff (ssh keys, data, etc.) is anyway probably running under/owned by that user.