hmm, which kernel do u have at the moment? u can find the stock kernel on xda forum, u dont have to back it up.. download it, and just flash it after u've rooted the insecure kernel. u can find it here

[ROM + Guide]Official i9100 Firmwares KF1/2/3/4/, KG1/2/3/5/6/7, KH1/2/3 Download - xda-developers

however, if ur planning on rooting, i'd recommend the CF root method. this way, u dont have to flash an insecure kernel and root it, then flash back stock. u just flash the CF root kernel which is (obviously) already rooted. u still need the stock kernel though, which u can find on the above link. the CF root stuff and guide is here:
[17.08.2011][CF-Root v4.1] KE2/7/8, KF1/2/3/4, KG1/2/3/5/6/7, KH1/3 - su+bb+CWM4 - xda-developers

 

i dont know of any such program and i dont think its necessary i understand ur worried about changing anything with ur new phone, but intratech (the user on xda forum) posts 100% stock kernels and firmware, and no one has had any issue with them, so dont worry about it.