We have finally found a way to put LTIB under source control (SVN in our case).
While I was googling for that topic I have found a discusstion in LTIB mailing list, where it is said that "LTIB is intended more as a package publishing tool, not a software development tool so it should not be used for revision control" 
But anyway we would like to have all our modifications in SVN 
There were two problems for us:
- Install LTIB on Ubuntu/Kubuntu 12.04
- LTIB stores patches outside of directory where it is installed (by default /opt/freescale/pkgs)
First problem has been solved by my colleague with set of scripts, that he has found somewhere in the internet. These scripts don't solve all problems so he has added couple of his own scripts. Now it works fine for our BSP 20100413 for MPC8308ERDB and Ubuntu/Kubuntu 12.04. Zipped tarball with scripts is attached to this post and there is an original readme file inside.
Second problem has been solved in following way. I have added new parameter "our_patches" to ltib script. This is directory where I want to put all our patches. I have found a subroutine that implements "patchmerge" command and replaced lpp parameter with our_patches parameter. So now ltib put new patches in our-patches directory. Also I have added our-patches to ldirs definition. ldirs is a list of directories where ltib looks for the files. Also you need either to comment ldirs definition in .ltibrc file or to add our-patches there too.
ldirs => "$top/our-patches", our_patches => "$top/our-patches",
So now we can just pur all LTIB directory (after clean and without rootfs directory) under version control.