the strength of any weld repairs depends upon the person and experience they have. A good welder's repair should be as strong as the origional. When instigating the repair, the metal in most cases will be slightly thicker than origional and additional strengthening can be included. If your worried about flex affecting the repair then replace the cills with box section as this will reduce the flex through the floor. As for cost this can be anything, do it yourself and it only costs time and the sheet metal, pay someone else and the cost will be slightly more.
Thanks for the advice re small angle grinder. I've got a jigsaw but what is a reciprocating saw??