This is one of the first "apostate" claims I came across here and on JwFacts (back when I was lurking years ago) that I gave a lot of thought to, probably because I was beginning to think about investing at that time myself (so I was learning about investments).
I also don' think the investments made by the Watchtower really matter much. One of the best ways to invest (in my opinion) is in index funds. By definition index funds try to mimic the entire investible market (or some broad segment of it) (i.e. Total US Stock Index, S&P 500, etc). Both these indexes hold Phillip Morris (tobacoo/cigarettes). Even if one doesn't invest in index funds, most large stock funds will include Phillip Morris.
I don't really see holding thousands or hundreds of companies, and having a few that are "immoral" would be much differnet than an employee working at a grocery store and sometimes has to check out customers that buy cigarettes. The latter example is "approved" by the org.
That said, if they turn around and judge the Catholic Church or other religions for investing in said companies in a manor similar to the way the JW organization does, then, well, ... that is a problem, I would agree! But only a problem for being hypocritical, not for there being some intrinsitc issue with investing in funds that have a small handful of defense/tabacoo/etc companies.
After all, if one is going to get all worked up and say they shouldn't invest in broad market funds because of the defense/tabacoo companies, then perhaps they shouldn't invest at all since it would be in "the comericial aspect of satan's system", full of "greedy companies." Maybe a slippery slope arguement, but I just think WT investments is a non-issue.