Yes, that makes sense to me. With those quality scores, I think that's your only option.
(Maybe the sequencing core is willing to consider this a failed run and rerun it for you.)
...Unless you amplicons are much shorter than you expect. Is that possible?
I've seen read quality like than when we accidentally used a 250 bp paired-end kit to to sequence a <200 bp region of the 18S gene.
When a region has been fully sequenced, quality drops suddenly. Could this be happening with your data?