Read alignment using Bowtie2
One possible workaround would be to blast your sequences against the genome. Then, when you have found where they align, you can extract those regions only into a new fasta file (make sure to take a few kb around each target region) and then use that fasta file as the "genome" you pass to bowtie2.

That would give bowtie a far smaller file to work with and should reduce the memory needed significantly.