To start with, I should note that there's no such thing as the "subjunctive tense"; you really mean to ask whether your example "past indicative" or "past subjunctive". I mention this because the past subjunctive behaves as a past tense in some respects, as may be seen in an example like:
I'm sure he doesn't think that she is the one doing this.
If he thought that she was the one doing this, I'm sure he would say something.
The "was" is possible because a "sequence of tenses" rule with no "sequence of moods" rule; the past subjunctive "he thought" in the matrix clause licenses the use of a past tense in the subordinate clause, but not the use of the subjunctive mood, so we end up with the past indicative "she was the one". (That said, I think the past subjunctive "she were the one" would also be fine in this example.)
There's also a "present subjunctive", as found in e.g. "She demanded that he leave the premises", though the present and past subjunctives are really two separate moods, rather than being two tenses of the same "subjunctive mood". (For this reason, some authors introduce other terms, e.g. "irrealis mood" for the past subjunctive.)
The choice I made would also depend on whether I was directly involved with the project.
This is actually using the past indicative — what you referred to as "past tense" — but it's nonetheless completely correct, and your classmate is wrong to say otherwise.
You can tell that this is the past indicative (not the past subjunctive) by considering a similar example with the verb be, which is the only verb in the language that distinguishes the two:
OK: The choice I was faced with would also depend on […]
not: The choice I were faced with would also depend on […]
This use of "was" (or in your case "made") is because of the sequence-of-tenses rule that I mentioned above (but in this case triggered by the conditional mood rather than the past subjunctive); the main clause uses the conditional ("would depend"), so the subordinate clause needs to use a past-tense form. This is the same reason that you wrote "whether I was directly involved" later in the same sentence.
However, your classmate's suggestion ("The choice I would make") would also be correct, and might even be a better choice, because you're describing your (hypothetical) volition. The version with "The choice I made" subtly characterizes the choice-making as a mysterious event to be explained by reference to external factors, whereas the version with "The choice I would make" characterizes you as an agent of your own will. The latter is more consistent with the use of the word "choice". I might even suggest rephrasing the whole thing to emphasize your agency even further:
I might also make a different choice if I were directly involved with the project than if I were not.
He also left the following comment in regards to the final sentence in this excerpt:
This sentence is a little confusing. Also stop using past tense.
He's more-or-less correct here; he has the same confusion that you did regarding the term "past tense", but if his point is that you should use the past subjunctive rather than the past indicative — "if I worked for Google but were not going" rather than "if I worked for Google but was not going") — then he's completely right about that.
Incidentally, regarding this:
As a senior employee, I would have invested many years building my career and may have been at my current company for a long time.
The conditional of may is might, so you should write "might have been" rather than "may have been".
He lowered my grade on the paper because of this, so I would like to make sure that my grade is what it should be.
This is out-of-scope for this site, but if he lowered your grade by more than a token/symbolic amount, I think it makes sense to check with the instructor. I don't think that minor/debatable grammar issues should affect your grade in an engineering ethics course.