I had never heard of Milliput, so looked it up. A couple of things bothered me about "it's" use and this particular use.
Firstly, it would seem that Milliput was a particular product, but now, Milliput has become the generic name for a whole range of products which are basically epoxy putty. To quote from their own web site...
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it has already passed into our technical vocabulary as a blanket term for epoxy resin putty.
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... thus saying "Milliput" is like saying "silicone sealant". There would appear to various manufacturers and grades. Some may be suitable for aquarium use, others not.
The other issue I found looking was this quote, also from their website...
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but note that Milliput is not intended as a thin layer adhesive and should not be used where a paste, mucilage or thin glue is indicated.
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... would seem to me to indicate that it is not particulaly well suited to gluing stones/rocks together.
I would recommend that you use an aquarium rated silicone sealant, or at least, that you contact the manufacturers of the product you have to seek clarification. There was a contact page on the genuine Milliput web site.