Thanks to John Marshall's help with interpreting the samtools segmentation fault, I was able to fix the error. Here is the code that I ended up using to put reads mapped to individual bacterial/phage genes from a multifasta file (a transcriptome bam file from kallisto) onto the bacterial/phage genome fastas from which the genes were taken (this is reinventing the wheel in a sense, since rsem-tbam2gbam and tophat - Transcriptomic Coordinate Bam To Genomic Coordinate Bam - already have utilities to do this, and is limited to bacterial CDS's):

from sys import argv

from Bio import SeqIO
from Bio.Seq import Seq

import pysam

gbfile = argv[1]
infile = argv[2]
outfile = argv[3]

bamIn = pysam.AlignmentFile(infile, "rb")

gb = SeqIO.parse(gbfile, "genbank")

gbInfo = []

header = bamIn.header
header['SQ'] = []
recCount = 0

#save information from the genbank file that is needed for modifying the BAM file
for rec in gb:
    header['SQ'].append({'LN': len(rec), 'SN': rec.id})
    for feat in rec.features:
        if (feat.type == "CDS" and "pseudo" not in feat.qualifiers.keys()):
            if feat.strand == 1:
                featInfo = [recCount, int(feat.location.start), feat.strand]
            if feat.strand == -1:
                featInfo = [recCount, int(feat.location.end), feat.strand]
            gbInfo.append(featInfo)
    recCount = recCount + 1


with pysam.AlignmentFile(outfile, "wb", header = header) as bamOut:
    for aln in bamIn:
        if( not(aln.is_unmapped) ):
            #Use the existing alignment as a template and edit elements of the alignment as needed
            alnOut = aln
            #Reverse-complement the sequence, reposition the read, and reverse the CIGAR for reads mapping to features on the negative strand
            #Modify the read itself 1st
            if gbInfo[aln.reference_id][2] == -1:
                #if the read maps to a feature on the reverse strand, then reverse complement the read sequence
                sequence = Seq(aln.query_sequence)
                revcomp = str(sequence.reverse_complement())
                alnOut.query_sequence = revcomp
                #adjust the leftmost position of the read if the beginning of the read is deleted or hard/soft clipped
                if aln.cigartuples[0][0] in [2,4,5]:
                    alnOut.reference_start = gbInfo[aln.reference_id][1] - aln.reference_start - len(aln.query_sequence) + aln.cigartuples[0][1]
                else:
                    alnOut.reference_start = gbInfo[aln.reference_id][1] - aln.reference_start - len(aln.query_sequence)
                #if the read maps to a feature on the reverse strand, then reverse the CIGAR code
                alnOut.cigartuples = alnOut.cigartuples[::-1]
                #change the sign on the insert length to indicate that the reads have swapped order
                alnOut.template_length = -1*aln.template_length
                #reverse the order of the quality string
                if alnOut.query_alignment_qualities:
                    alnOut.query_alignment_qualities[::-1]
            #Modify the paired read 2nd
            if gbInfo[aln.next_reference_id][2] == -1:
                alnOut.next_reference_start = gbInfo[aln.reference_id][1] - aln.reference_start - aln.template_length
            #Reposition reads mapping to features on the positive strand
            if gbInfo[aln.reference_id][2] == 1:
                alnOut.reference_start = gbInfo[aln.reference_id][1] + aln.reference_start
            if gbInfo[aln.next_reference_id][2] == 1:
                alnOut.next_reference_start = gbInfo[aln.reference_id][1] + aln.next_reference_start
            #Reassign the reference sequences
            alnOut.reference_id = gbInfo[aln.reference_id][0]
            alnOut.next_reference_id = gbInfo[aln.next_reference_id][0]
            bamOut.write(alnOut)

bamIn.close()