I haven't merged it into the master branch yet, but you can make bigWig files with pyBigWig in the WriterIntegration branch. That'd allow you to script something to fix the problematic line(s).
The fix would be something along the lines of:
lastLine = None
bw = pyBigWig.open("something.bw", "w")
for line in bedGraph.split():
if line == lastLine and line < lastLine:
#Do something appropriate
lastLine = line
bw.addEntries([line], [line], ends=[line], values=[line])
That'd give you a bigWig file and allow you to fix overlapping entries however you'd like.