Tuvok and Neelix were not in suspended animation in Tuvix. They were not like Barlcay in the particle soup of the transporter
deconstructed but still conscious. Someone remind me; did Neelix and Tuvok remember anything from their time as Tuvix?
Tuvix was like Frankenstein['s monster] -- a new being made of the parts of others no longer alive/cognizant themselves. Right here, right now, Tuvok and Neelix aren't thinking and feeling self-aware beings but Tuvix is. And Janeway's duty is to protect him even if it isn't convenient for her ship, even if she misses her friends, and especially because he has no one else to defend him in the whole universe. Right then right there, Tuvix is a being in his own right -- with his own right to LIFE, liberty, and the pursuit of happiness.
It may have been an accident that made him, but that wasn't, by definition, in their control. What they did then
was. What they did then was harvest Tuvix to recreate Tuvok and Neelix, no different than, as mentioned, if the state (or some corporation) started harvesting the organs/lives of some of its citizens (or employees/shareholders) to help larger numbers of others alive now or yet to be.