Filtering out reads from a reference (e.g. rRNA) using bowtie2
If you want to remove rRNA, use tools that are made for this. We usually go for SortMeRNA, which can do exactly what you describe your goal is, i.e. go from FASTQ to FASTQ, splitting your reads into rRNA and non-rRNA.
In our experience, it is very accurate, if a bit slow at times.