Given the hardcoded config, the first thing I would try would be whether putting a comma-separated list of the connames into that config will work. That will be dependant on the product reading the config. It may balk at the comma in the middle, or if you're lucky it will just take the whole string and pass it through to the MQ Client at which point all is well.
If that doesn't work, then you'll have to look into changing Datastage to use a different client configuration method, like the CCDT which will be more of an upheaval, hence trying the above first.
Cheers,
Morag