...I think the real debate is whether the game should follow a realistic approach or not. I honestly don't care either way, but I think a fair suggestion is starting players at 2.5 FT skill (between pitiful and awful) and then, as others suggested, have 1 FT pop for every 4-5 in JS.
The only reason to bring up actual statistics is that many people are making the argument that it is unrealistic to have good jump shooters be poor free throw shooters. Well how do we decide what is realistic? Cherry pick a few examples that support our case? No, that's lame. As is just stating, "anybody who plays knows this."
Instead, we collect a bunch of results from the real world ask: how common is it that good jump shooting goes along with good free throw shooting. And the answer is, contrary to everyone's gut feeling, the two don't go that well together. So your suggestion of adding 1 FT per 4-5 JS doesn't reflect real world results. There was a very slight tendency for good 3 point shooters to be better FT shooters, but it wasn't that strong either.
However, what the statistics do show, is that there is a certain floor of free throw percentage. Even the worst FT guys make at least 30-40% of their shots. In that case, if realism is your goal, suggesting that every player starts with pitiful or awful FT is quite reasonable. There's also ceiling effect as well; not too many guys are hitting above 92% (not sure what the upper levels of BB players is - surely nobody ever complained about it!).
The idea of having FT skill decay like stamina is cool too; one of the articles I read about FT shooting noted how many coaches hate to spend practice time on FTs, and will only do it when the FT% falls below a certain rate). This would also fit with your statement that the real world statistics are marred by practice.
Now all the above rests on the premise that the statistical results in BB should not be too far away from real life(i.e., they should be realistic). I don't see it that way, and would prefer to leave the FT shooting as it is, and force managers to make the strategic decision of when to spend a week training FT.
But, even for those people arguing that this unrealistic situation should be changed, linking FT to JS (or JR) doesn't accomplish your goal.