The word yet in your example sentences could be Merriam-Webster's sense 2c:
2c: at a future time : eventually
or sense 3:
3: nevertheless, however
M-W gives several sentence examples for yet, but none of them use the comma, regardless of the sense (except the one in which yet is part of the phrase "at least not yet"):
I haven't read the book yet.
Has the mail arrived yet?
It's not time to eat yet.
“Are you ready?” “No, not yet.”
We don't yet know what their plans are.
Their suggestions won't be implemented, at least not yet.
We don't have a firm grasp of the situation yet.
The first three example sentences use the word in sense 2c. There don't seem to be example sentences where the meaning is strictly that of "nevertheless, however."
It is not clear to me that the commas change the meaning in any of your examples. If you wanted to emphasize the feeling of "it hasn't happened now, but it could happen sometime in the future," you could use an em-dash. Grammarist has a great explanation and example:
Em dashes can replace colons or serve as harder versions of commas (similar to semicolons). While parenthetical em dashes often operate in pairs (see the examples under the first point above), hard-comma em dashes often function alone at ends of sentences, for example:
The all-renewable energy sector is 30 years away — and always will be. Salon
It’s that time of year again—time for New Year’s Resolutions! Pegasus Books
So, your example sentence could read
We're not dead — yet.
to emphasize the "not now, but perhaps soon" meaning of yet. While it doesn't change the meaning of the sentence per se, it does emphasize yet.