See http://www.w3schools.com/css/css_boxmodel.asp
It doesn't sound as if that will work as the css width is content only and the padding is in addition to.
So if you are specifying the content to 100% and the padding is 5px, then the total is 100% + 5px.
It sounds as if you really don't need the padding in this situation as it is the only element in the td, so I might consider overriding the inherited padding value on the element, at least the left and right such as:
<input type="text" style="width:100%; padding-left:0px; padding-right:0px;"/>
Another approach would be to use a slightly smaller percentage such as 95% or 90%.