Do you wan't to do the mapping with Lifescope or BWA? If you are using Lifescope, mabye there is an option in there to do the trimming. Lifescope supports clipping of the reads, by default it is enabled and it should remove a lot of the noisy tails of the reads.
Other than lifescope there are almost no tools that work directly with the SOLID native XSQ format. There are a couple of tools that convert XSQ to csFastq or csFasta. I also wrote one that support hard trimming of reads.
Once you have the data in csFasta or csFastq you could do the trimming if you find a tools that support the solid color space version of fastq and fasta. I am not sure if you then can convert back to XSQ, I think there is a tool from Life but I don't know if it works.