Just so you have the perspective right, a healthy TMD22 as installed by Amel will drive a clean hull Super Maramu at 8 knots at full throttle and 3000 RPM, and 7 knots throttled back to a sustainable cruising RPM of 2300 or 2400. If your top speed is 6, you are loosing a LOT because you really don't want to drive this engine at full throttle for hours at a time.
The conversion you are talking about is much more complex than just removing the turbo, but I'll assume you can find all the bits and pieces to convert the engine to a naturally aspirated engine. I think you'll end up with a Perkins M60--more or less. Do you know if the injectors or injection pump have been jiggered as part of making this into a turbo engine? I do not know for sure, but I'll bet they have. But assuming ALL that...
Now you have a 60HP engine (more or less) and a serious mismatch between the prop and the engine. You are what is know as "over-propped". Running 2000 RPM at full throttle with this engine is lugging it very badly. It is not putting out the power it is capable of and there are lots of reasons why this is very bad for a diesel engine.
You will need to re-prop the engine to get it running at a maximum rpm that is approaching specification. By the time you are done getting the parts you need for the conversion, and a new propeller, you will have spent as much--or more--than you would to have get the turbo fixed, and you will have a boat that doesn't perform as it should.
If all that doesn't convince you, and you can solve all those issues... you'll be killing the resale value of your boat by gelding its iron stallion.
I hate turbos too, but... an underpowered boat is not going to be a happy boat.
Get the turbo fixed, or replaced, and then take good care of it. It is not as fragile as some people make it out to be. More of them fail from abuse and lack of maintenance, rather than any inherent design flaws.
The WORST thing you can do to a turbo charger is start the engine, and immediately run it at high speed before the oil has had a chance to circulate and warm up to operating temperature. The bearings will be dry, or nearly so, and at the speeds a turbo spins, the bearings will die a very quick death.