Just my own opinion here... so take it for what it's worth.
I sucked my thumb openly until I was about 9 yrs old. (then it went into hiding!!

) The only reason I stopped doing it in front of people is b/c my 3rd grade teacher made fun of me in front of the whole class. (now I don't remember exactly what she said... and it's possible it was very mild... but all I remember is how I felt- ashamed)
Everyone in my family tried to get me to stop. Convinced I would have bad teeth, an overbite, what-have-you. But to no avail I continued. I can remember to this day the comfort I got from that sweet (and probably nasty!) thumb and my dear "miney" (which was any rag I could get ahold of to rub my nose with!). It was my best friend... always there and never ever did me wrong.
Can I please say- that not only did I NEVER have to have any dental work (ie- braces, retainer, etc...), I don't even have the slightest overbite. And I'll be honest- I was A LOT older when I stopped my secret habit.
Please think about how she actually feels about her thumb (that sounded silly when I re-read it but I still mean it!). There will come a time when she's had enough... but the person's comment before me was right. When she's ready there won't be an issue. Does she have any other security items around? My oldest daughter would not take a paci or her thumb. (I was her paci!!) However- she HAS to have my hair in her fingers before she can fall asleep. (she's 4 1/2) My youngest (2 1/2) has a paci, a bear, a blanket, AND she HAS to have a finger in my mouth before she can fall asleep. (or her daddy's!!) Talk about some ridiculous habits! (at least to me- but deinitely not to them!!)
My advice is to leave her alone. Perhaps you can persuade her to make sure her hands are washed before the thumb pops in... but I know how unrealistic that may actually be. You clearly sound like you are concerned about her well-being... and not just trying to "pull the plug!"
I hope this helps... and I didn't offend anyone. Again... only my opinion but from my own personal experience.
Oh how I loved that thumb.