I am using freebayes and bwa-mem together to align and call variants on my sequencing reads. But I am doing some editing to the reads before aligning and calling variants. I want some loci to be ignored based on my edits.

So if for example I have a base whose WT is G, but for a given read I see an A, if I change that A to an N will the sequence then be properly aligned to the genome but freebayes will not report any info for that locus, such that I won't see the variant, but I also won't see a read supporting the WT sequence?
If your sequencing data has quality scores (FASTQ), you should set the quality of the base to a very low value (depending on how your quality scores are encoded). The mapper will know to ignore it.

You can set the base to N, or you can even leave it as-is and hope the mapper maps it with mis-matches (which it should), but dropping the quality is probably the best way.

Even better would be if you edited the genome you're mapping too ;)