Ethics of staying in PhD program with no intention of being an academic, and misleading my advisor about this My field is extremely competitive for tenure track jobs that I: 


will most likely be unable to land after graduation
don't even really desire anymore.


In comparison to my classmates, my research productivity is absolutely pitiful. It is stymied by an apathy for my subfield and academia in general that has developed over my 2 year tenure in the program. 

Problem is, I can't get the industry jobs I want right now due to underdeveloped programming skills and inadequate networking. My best bet is to stick around and beef these up until I see an opportunity to leave. 

If I drop out now with my master's, I will have to start out at square one and get entry level work that uses none of the skills I have developed (we're talking competition w/ HS grads).  

However, I have already told my advisor about my doubts for a future in academia. They approved an academic leave request due to some issues in my personal life. At the end of my leave period, I have to tell my advisor that I wish to complete the program and stay in academia. 

On one hand, my situation is not so different from any other PhD student forced to go alt-ac due to disinterest or poor performance, but on the other hand, I will have to mislead my advisor to return. 

I only want to continue at this point for job prospects, and my advisor won't be inclined to take me back if I tell them this.  

I am willing to pick up the pace with my research and get the PhD, so it won't be a complete waste for my advisor, but it will still be largely a waste of their resources. 

A similar question by another PhD student can be found here - When is the right time to tell my advisor that I plan on leaving my PhD program?
As a PhD student, you don't have to want an academic career. It's not unethical to pursue a PhD with no intention of staying in academia afterward. 

But lying about your plans and deliberately misleading is wrong and unfair to your advisor. 

You wrote:


  However, my advisor seems to be especially invested in making me a viable academic researcher because I am their first student and have used a lot of their startup funds. My field is also not typically industry-bound like, for example, engineering, so any reputation boost my advisor could hope to get from me is nil. 


If your advisor is a new professor whose own career success really depends on graduating PhD students who go on to academic careers, letting them invest everything in you under false pretenses is obviously wrong and unethical.

It sounds like you don't really want to finish your PhD (I infer this from your "apathy for my subfield and academia in general"), and you think your advisor wouldn't want you to stick around for a few more years under the circumstances, either. On the other hand, finishing out the academic year - giving you time to look for a job, and giving your advisor time to find another PhD student in this application cycle, while you wrap up and publish your current work - sounds like a win-win. But you should tell your advisor right away, so that the two of you can make informed plans for the future. 

I suggest you come up with a plan for preparing yourself for the job market during this academic year, then have that talk with your advisor, and make the most of your remaining time.

On the other hand, if you really do want to finish your PhD, tell your advisor that you're not interested in academia, but are interested in finishing your PhD and getting a job that takes advantage of your PhD-level research skills. (Many of the skills acquired by successful PhD students are fairly transferable.) Your advisor may be more willing to support you than you think - successfully graduating PhD students is important for new professors, even if the student isn't interested in academia in the end. But you need to let your advisor make that choice: lying to someone so that they will give you multiple years of research support just so that you can buy time to train yourself for an unrelated career, is wrong.