I would think that a multi-step process would work:

1. Filter for reads overlapping an exon
2. Filter those passing step 1 for those overlapping an intron
3. Filter those above for more than 1 CIGAR operation (you could filter out spliced alignments instead, but there's not then a simple samtools view option...this is quick and easy and close enough).

I'm not sure if I understand well, your problem: you want the cigar section ('M' or 'X' or '=') overlapping the BED file isn't it.

Here is a solution using http://lindenb.github.io/jvarkit/SamJdk.html

private List<Interval> intervals=null;
public Object apply(final SAMRecord record) {
    if(this.intervals==null)
        {
        /** first call: we load the BED file "junction.bed" */
        try
            {
            java.io.BufferedReader r=new java.io.BufferedReader(new java.io.FileReader("junction.bed"));
            this.intervals = r.lines().
                filter(S->!(S.isEmpty() || S.startsWith("track")|| S.startsWith("browser"))).
                map(S->{
                    final String tokens[]=S.split("[\t]");
                    return new Interval(tokens[0],1+Integer.parseInt(tokens[1]),Integer.parseInt(tokens[2]));
                    }).
                collect(Collectors.toList());
            r.close();
            }
        catch(Exception err)
            {
            throw  new RuntimeException(err);
            }
        }
    // ignore unmapped
    if(record.getReadUnmappedFlag()) return false;
    final Cigar cigar = record.getCigar();
    if(cigar==null || cigar.isEmpty()) return false;
    // loop over the cigar string
    int pos = record.getStart();
    for(final CigarElement ce: cigar)
        {
        final CigarOperator op= ce.getOperator();
        if(op.isAlignment()) // it's 'M' or 'X' or '='
            {
            // search overlapping our bed list
            for(final Interval r:this.intervals)
                {
                //found !
                if(r.getContig().equals(record.getContig()) &&
                    pos <=r.getStart() &&
                    (pos+ce.getLength()) >= r.getEnd())
                    {
                    // accept this sam record
                    return true;
                    }
                }
            }
        if(op.consumesReferenceBases())
            {
            pos+=ce.getLength();
            }
        }
    // we don't accept
    return false;
    }

usage:

java -jar  dist/samjdk.jar -f biostars292561.code --body input.sam