Doing a full discharge of a lithium battery isn't exactly healthy for them, Usually most devices have multiple levels of protection - typically tripping the on-battery protection is one of those "in case all else fails" things.
The last time I pulled apart a Lithium Ion cell, the plastic "case" was <1 mm thick and glued directly to the battery. Destructively (and carefully) cutting/melting the case was the only way to get at the internals.
Anyway, just keep an eye on it, and when recharging it back up, be sure to go through the low-current "precharge" first.
James