I grew up in a family of smokers, I have asthma and mum died from smoking.
I have a 16 week old and I must admit I was utterly paranoid about the smoking thing, as many people in both our families smoke, and the idea of asking MIL to not come in smelling of smoke really wound me up because everything that is different to what was done in her day was a trial.
I asked all smokers not to smoke prior to coming in the house, and that they couldn't nip out for a "break" while they were here too. BUT I do think you are being over the top on the clothing side of it.
I am not defending FIL he has acted like a fool, but some people do overreact like that when embarrassed/offended. Either way, he's in the wrong.
But I say it for your own piece of mind. The guidelines are there to keep baby safe and healthy and to make sure baby doesn't come into regular contact of things that harm them, especially with households that have smokers.
As for a t shirt, as long as the person doesn't come in after just smoking, you need to think about the chemicals and yes, they will be present, BUT you need to think about the concentration in the air if you walk past busy roads, people smoking on the street....etc, things need to be put into to perspective. Yes I wouldn't be too jolly about baby nuzzling her face into a smokers clothes, but a quick hold and a coo over her, it's minuscule.
But, your baby your choice. No one can say what you are doing is wrong, because it's better than being the polar opposite and being completely complacent.