I realize that this is a very old post, but I'll give my 0.2c anyway...
The only reason I would use Java over Perl is if my MQ Server requires a certain userID to be used for security reasons. With Perl and C, the userID of the client is passed on to the server and to the best of my knowledge, there's no getting around that. With Java, you can specify the userID of your liking.
Apart from that nuisance, I found that it's very easy to work with MQSeries through Perl and posted a write-up about it at usestrict.net
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