This has improved with new features in version 9.5.11.
See https://www.ibm.com/support/knowledgecenter/SSQL82_9.5.0/com.ibm.bigfix.doc/Platform/Config/r_client_set.html?view=kc#r_client_set__amgt , specifically the _BESClient_ActionManager_OverrideTimeoutSeconds and _BESClient_ActionManager_OverrideDisposition client settings.
The global settings are intended to allow the client to ‘eventually’ start responding again in case an action spawned with wait or waithidden are never going to complete, for instance if they are trying to display a message that can not be acknowledged because the process does not have a desktop window. Ideally this value should be set at an hour or higher, and even longer when doing long-running operations such as an OS reinstall.
For individual actions, where you might want the timeout to be shorter, there are also now override options that can be used, per https://developer.bigfix.com/action-script/reference/execution/override.html
override wait
timeout_seconds=360
disposition=terminate
wait program.exe