I don't see lock-in issues as a concern. It's an open spec, if it becomes popular enough then even if other browsers don't want to support it developers can make plugins for those browsers (some of the papers even mention this, I believe). In any case, if websites require you to use NaCl it is only stupid unless they are doing something that otherwise wouldn't be feasible e.g. running a performance hungry emulator. It's clear to me that Google has no intentions to leverage this for lock-in.

If other browsers are forced to add NaCl support: of course I doubt they will have the same security, performance and compliance that Chrome does -- but who are we kidding, it's highly unlikely that all browsers will ever be equal in those ways.