Which word could be eliminated from the sentence: "Time, as a matter of fact, is up." for a stronger effect?
I would actually eliminate several words. I would take out "as a matter of fact".
"Time is up" is much shorter, and in my opinion, shows the panic that one feels when told that time, is indeed, up.
I find "Time is up.", being a much shorter sentence when removing "as a matter of fact" (a subordinate clause), parallels the message of the sentence.
Having a short sentence in the middle of multiple longer ones puts a break in the overall pacing of the sentences, and asks the reader to consider the short sentence more closely.
Thus, it puts greater emphasis on the fact that "time is up" and puts the reader in the speaker's shoes.