path/filepath を使って安全に。
package main

import (
    "fmt"
    "path/filepath"
)

func replaceExt(filePath, from, to string) string {
    ext := filepath.Ext(filePath)
    if len(from) > 0 && ext != from {
        return filePath
    }
    return filePath[:len(filePath)-len(ext)] + to
}

/* Example */
func main() {
    filePath := "inputDir/input.csv"

    fmt.Println(filePath)
    // => inputDir/input.csv
    
    filePath = replaceExt(filePath, ".csv", ".json")
    fmt.Println(filePath)
    // => inputDir/input.json
    
    filePath = replaceExt(filePath, ".json", "")
    fmt.Println(filePath)
    // => inputDir/input
    
    fmt.Println(replaceExt("inputDir/input", ".csv", ".json"))
    // => inputDir/input

    fmt.Println(replaceExt("inputDir/input.rcsv.csv", ".csv", ".json"))
    // => inputDir/input.rcsv.json
}