I have .46 sizelow winger and I was wondering if I can put my .61 size engine in it or not?

Sure you can. Should be a good combo. You'll be able to practice up on throttle managemant as well as enjoy the benefits of surplus power...as long as it fits. My .46 size Lanier Extra flies great with a Magnum .61. Enjoy.

But is there any risk of plane disintegrating with so much power?

Well, possibly. I put a 61 MDS in a sport flier 40. This is an ARF and i didn't check the glue joints. The end result was the bulkhead an engine departed the plane after a high speed pass. I think if you check the plane out and maybe beef up suspect areas u should be ok.

Guess I'd ask, 'which 40 size low winger?'

Many (most?) will handle the power fine, but you should also figure out how you'll balance it with all the extra weight.
Dennis-

Physically yes...

Extra power (even if you never need to use it) is good to have in case you have to power yourself out of trouble. Saved me a few times. If I hadn't had the power, my planes would have become "tree food".

BUT! I've also seen newbies with lots of extra power get into trouble, hit full throttle, then hit the dirt with twice as much speed, destroying a plane that would have been easily repaired if they'd killed the throttle instead.
Dennis-

If it is an ARF, I would think twice about it. If you do it, go in and put some 1/2 inch triangle stock on the firewall to the side walls and bottom. Also go back and double glue all the formers in the fuse and the top and bottom sheeting where you can. If it is a build up, look it over well and make sure it is strong enough.

Gentlemen, we're talking about a .61 on a .46 size airplane. If we add glue and reinforce every joint to which we have access the advantage of the .61 is negated. It's not like we're adding a John Deere engine here. Gimme a break!