I suppose the meeting is over now, and the decision has been made, one way or the other. I am a little bit puzzled as to why you have to weld new doubler plates/pads onto the Boom, weren't there Doubler Plates for the old wire guides, that could be re-used?
Anyway, cover your ****, make sure you keep copies of emails to and from your Super regarding this job, just in case you end up in Court and the Super develops slopey shoulders.
Maybe even send him an email summarising your understanding of the agreement made at the meeting today, and asking him to confirm it. That will place him on the Hot spot and he won't be happy, but is normal ashore, where meetings are minuted and copies sent to all participants for review. It makes sure everyone involved has the decisions made in Black and White and can refer back to them later in case of any misunderstandings.
The Marine Industry lags far behind shore side in documenting decision making, possibly because many Marine Engineers have some difficulties with paperwork and are used to making their own decisions rather than working through a committee.
Regarding contacting Class Directly that is certainly dangerous, for you, if the Super has decided not to contact them. However, the Contract between Class and your Shipping Company will clearly say that it is the ship owner's responsibility to call in Class if there are any failures of, or repairs to, any Classed items.
In this case is the crane Classed?? Not all are.
However, Flag state have responsibility for everything that goes on on board, you don't say if your ship is UK flag or not, but I assume from your personal details that you are in Scotland at present, presumably working in the North Sea Offshore Industry. There is a possibility of contacting the MCA if you feel the repair would be dangerous/ unsafe but again your Super will see this as undermining his Authority and knowledge.
There is a possibility that rather than welding the doubler to the Boom you could clamp it on, maybe a bit more expensive to fabricate a bolted clamp that size, but it avoids all the risks of welding, and then weld the guide onto the bolted clamp.
I would certainly discuss this with the Captain of the ship, he is also responsible for the safety of the Ship and the people on board, and it is your responsibility to keep him informed of any safety or reliability issues that are concerning you. It is always useful to discuss things like this with the Captain, he knows the people and Companies involved and is experienced in the industry. As the old saying goes, " a trouble shared is a trouble halved". If you discuss the problems you are having in your Department with the Captain he will have much more confidence in you than if you just tell him everything is perfect all the time.
A lot depends on the shipping Company and your Super, also the Class Surveyor you contact, if a Surveyor turns up, out of the Blue, and starts raising hell the Super will be blaming you for dropping him in it, and it won't advance your career prospects at all.
Good Luck and let us know how it works out.
It is always better to ask a stupid question than to do a stupid thing.