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Currently, when using SDL_HINT_RENDER_SCALE_QUALITY linear, a texture is filtered with respect to the pixels outside of the source rectangle. I don't know how rational this is, but in my opinion when using a srcRect, the linear filter should not blend with pixels of the texture outside the srcRect.
The following code demonstrates this effect.
A half red and half blue square is created. The srcRect is set on just the red half. Using SDL_SetHint(SDL_HINT_RENDER_SCALE_QUALITY, "linear") still shows blending with the blue half. Commenting out the hint obviously shows the nearest pixel sampling method. This is how I would expect the result to look when using a srcRect regardless of the SDL_HINT_RENDER_SCALE_QUALITY value.

/////CODE
#include <stdio.h>
#include "SDL.h"

#if SDL_BYTEORDER == SDL_BIG_ENDIAN
static Uint32 rmask = 0xff000000;
static Uint32 gmask = 0x00ff0000;
static Uint32 bmask = 0x0000ff00;
static Uint32 amask = 0x000000ff;
#else
static Uint32 rmask = 0x000000ff;
static Uint32 gmask = 0x0000ff00;
static Uint32 bmask = 0x00ff0000;
static Uint32 amask = 0xff000000;
#endif

int main(int argc, char *argv[]) {
    
    if (SDL_Init(SDL_INIT_EVERYTHING) < 0) {
        printf("Could not initialize SDL\n");
        return 1;
    }
    
    SDL_SetHint(SDL_HINT_RENDER_SCALE_QUALITY, "linear");
    
    SDL_Window *window = SDL_CreateWindow("Title", SDL_WINDOWPOS_UNDEFINED,SDL_WINDOWPOS_UNDEFINED,500,500, SDL_WINDOW_SHOWN);
    SDL_Renderer *renderer = SDL_CreateRenderer(window, -1, 0);
    
    SDL_Surface *surface = SDL_CreateRGBSurface(0, 10, 10, 32, rmask, gmask, bmask, amask);
    SDL_FillRect(surface, &(SDL_Rect){0,0,5,10}, SDL_MapRGBA(surface->format, 255, 0, 0, 255));
    SDL_FillRect(surface, &(SDL_Rect){5,0,5,10}, SDL_MapRGBA(surface->format, 0, 0, 255, 255));
    SDL_Texture *texture = SDL_CreateTextureFromSurface(renderer, surface);
    SDL_FreeSurface(surface);
    
    SDL_Rect src = {0,0,5,10};
    SDL_Rect dst = {0,0,250,500};
    
    SDL_bool running = SDL_TRUE;
    while (running) {
        
        SDL_SetRenderDrawColor(renderer, 0, 0, 0, 255);
        SDL_RenderClear(renderer);
        SDL_RenderCopy(renderer, texture, &src, &dst);
        SDL_RenderPresent(renderer);
        
        SDL_Event event;
        while (SDL_PollEvent(&event)) {
            if (event.type == SDL_QUIT) {
                running = SDL_FALSE;
                break;
            }
        }
        
        SDL_Delay(100);
    }
    
    return 0;
}