Now when you want to have a thread do some work, send back results to the mainloop and continue running but the mainloop controls when the thread should stop working, you need some extra flags. This is an example of how you might use ecore_main_loop_thread_safe_call_async() and pthreads to do this.
//Compile with:
//gcc -o efl_thread_4 efl_thread_4.c -g `pkg-config --cflags --libs elementary`
#include <Elementary.h>
#include <pthread.h>

static Evas_Object *win = NULL;
static Evas_Object *rect = NULL;

struct info
{
   double x, y;
};

static void my_thread_mainloop_code(void *data);

static pthread_t thread_id;
static pthread_mutex_t th_lock;
static int th_exit = 0;

// BEGIN - code running in my custom pthread instance
//
static void *
my_thread_run(void *arg EINA_UNUSED)
{
   double t = 0.0;

   // inside the pthread function lets loop forever incrementing a time point
   for (;;)
     {
        struct info *inf = malloc(sizeof(struct info));
        int do_exit;

        if (inf)
          {
             inf->x = 200 + (200 * sin(t));
             inf->y = 200 + (200 * cos(t));
             // now call a function in the mainloop and pass it our allocated
             // data that it will free when it gets it
             ecore_main_loop_thread_safe_call_async
                (my_thread_mainloop_code, inf);
          }
        // and sleep and loop
        usleep(1000);
        t += 0.02;
        // in case someone has asked us to cancel - then cancel this loop
        // co-operatively (cancelling is co-operative)
        pthread_mutex_lock(&th_lock);
        do_exit = th_exit;
        pthread_mutex_unlock(&th_lock);
        if (do_exit) break;
     }
   return NULL;
}
//
// END - code running in my custom pthread instance

static void
my_thread_new(void)
{
   pthread_attr_t attr;

   pthread_mutex_init(&th_lock, NULL);
   if (pthread_attr_init(&attr) != 0)
     perror("pthread_attr_init");
   if (pthread_create(&thread_id, &attr, my_thread_run, NULL) != 0)
     perror("pthread_create");
}

static void
my_thread_mainloop_code(void *data)
{
   struct info *inf = data;
   evas_object_move(rect, inf->x - 50, inf->y - 50);
   free(inf);
}

// just test cancelling the thread
static void
down(void *data EINA_UNUSED, Evas *e EINA_UNUSED, Evas_Object *obj EINA_UNUSED, void *event_info EINA_UNUSED)
{
   pthread_mutex_lock(&th_lock);
   th_exit = 1;
   pthread_mutex_unlock(&th_lock);
}

// on window delete - cancel thread then delete window and exit mainloop
static void
del(void *data EINA_UNUSED, Evas_Object *obj, void *event_info EINA_UNUSED)
{
   pthread_mutex_lock(&th_lock);
   th_exit = 1;
   pthread_mutex_unlock(&th_lock);
   evas_object_del(obj);
   elm_exit();
}

EAPI_MAIN int
elm_main(int argc EINA_UNUSED, char **argv EINA_UNUSED)
{
   Evas_Object *o;

   elm_policy_set(ELM_POLICY_QUIT, ELM_POLICY_QUIT_LAST_WINDOW_CLOSED);

   win = elm_win_util_standard_add("efl-thread-4", "EFL Thread 4");
   evas_object_smart_callback_add(win, "delete,request", del, NULL);

   o = evas_object_rectangle_add(evas_object_evas_get(win));
   evas_object_color_set(o, 50, 80, 180, 255);
   evas_object_resize(o, 100, 100);
   evas_object_show(o);
   // new in the examples - we have a mouse down on the blue box cancel
   // the thread
   evas_object_event_callback_add(o, EVAS_CALLBACK_MOUSE_DOWN, down, NULL);
   rect = o;

   // create custom thread to do some "work on the side"
   my_thread_new();

   evas_object_resize(win, 400, 400);
   evas_object_show(win);

   elm_run();
   pthread_mutex_lock(&th_lock);
   th_exit = 1;
   pthread_mutex_unlock(&th_lock);

   return 0;
}
ELM_MAIN()