I think the interpretation (and whether it's viewed positively or darkly) strongly depends on the philosophical position and beliefs of whoever reads it.

It invites the reader, who is expected to know a bit about software technology, to interpret a few common commands as symbolic for the end of a life. But when you say something like "rest in peace", those words are understood in a tradition and the expected interpretation is set. When you say "rest in peace", hardly anyone will get offended and suggest that you're implying the person was too loud in life - even though someone may choose those words for exactly that reason, somewhat disrespectfully.

In this case, the correct interpretation is not a given and you are invited to take these commands and complete the analogy yourself. `git push origin final` is a command that tells version management software which is all but universal in software development, called Git, that what is in the project right now and which has been labeled as 'final' should be uploaded to a remote location called 'origin'.

In Git, the name 'origin' is typically given to the location where the code originally came from, or the place which the developer has designated as the primary location where this code lives in the world, to be shared with others. So, a possible interpretation is that the final state of being of the deceased is being uploaded to where they came from originally, but another would be that they have completed their final contribution to the world, where they lived their life. If you're more about reincarnation, pushing 'final' to 'origin' also works nicely because it feels circular.

The double ampersand `&&` indicates that after the first command, the second command will be executed, `rm -rf /`. That command, provided the user has the authority to do so, wipes everything on the computer, leaving nothing. `rm` stands for 'remove' and `-rf` indicate that everything will be removed recursively, and forcefully. The slash at the end means the 'root' of the system, it's like the roots of a tree, holding up the trunk and all the branches, everything on a Linux computer lives in `/`.

The command might be interpreted as destroying all that is physical, wiping their presence from the planet - for me it evokes the idea of cremation or disappearing into nothingness after life has left the body. In context of the first command, it suggests that everything of value has already been passed along and it is a good idea to wipe the slate clean and not to cling to what is left behind. But again, the exact meaning to any one person will depend very much on their cultural ideas on our lives, our bodies, and what it means to die. To some `rm -rf /` may be more reminiscent of destruction, especially on its own, and could feel dark or angry. Given they were murdered, as you say, this may be insensitive and harsh to those close to your friend - as if a life can just be ripped out by 'deleting' a person and everything they are. If they had just posted `rm -rf /`, it would border on being offensive to many.

"Onwards to the source" is the most revealing about the author. It sounds spiritual and suggests they believe in some form of afterlife our greater reality beyond our own, that is meaningful. In the context of programming, the 'source' is the computer code that makes up anything real, the underlying reality of software, what was written by the designer - so in choosing that word, there's still a lot of room for interpretation.

I think your friend's colleague did a very good job, and I'm sure they wrote this thoughtfully, but it's unclear what their feelings were for the second part. Perhaps it's something they've taken from somewhere else, because I've seen similar statements in online fora as famous coders and computer scientists died over the years. But it's also possible it just came to them similarly, because it's definitely fitting for many.