Changes to main.c
66c66
< #define SEC_PARAM_BOND                  1                                           /**< Perform bonding. */
---
> #define SEC_PARAM_BOND                  0                                           /**< Perform bonding. */

Also tried to change the sd_ble_gap_sec_params_reply parameter as your first surgestion:
320c320
<                                                    &s_sec_keyset);
---
>                                                    NULL/*&s_sec_keyset*/);


Changes to ble_nus.c
106,107c104,105
<     BLE_GAP_CONN_SEC_MODE_SET_OPEN(&cccd_md.read_perm);
<     BLE_GAP_CONN_SEC_MODE_SET_OPEN(&cccd_md.write_perm);
---
>     BLE_GAP_CONN_SEC_MODE_SET_OPEN(&cccd_md.read_perm); // Has to be open, do not know why
>     BLE_GAP_CONN_SEC_MODE_SET_ENC_NO_MITM(&cccd_md.write_perm);
125,126c123,124
<     BLE_GAP_CONN_SEC_MODE_SET_OPEN(&attr_md.read_perm);
<     BLE_GAP_CONN_SEC_MODE_SET_OPEN(&attr_md.write_perm);
---
>     BLE_GAP_CONN_SEC_MODE_SET_ENC_NO_MITM(&attr_md.read_perm);
>     BLE_GAP_CONN_SEC_MODE_SET_ENC_NO_MITM(&attr_md.write_perm);
166c164
<     char_md.char_props.write_wo_resp = 1;
---
> //    char_md.char_props.write_wo_resp = 1;
178,179c176,177
<     BLE_GAP_CONN_SEC_MODE_SET_OPEN(&attr_md.read_perm);
<     BLE_GAP_CONN_SEC_MODE_SET_OPEN(&attr_md.write_perm);
---
>     BLE_GAP_CONN_SEC_MODE_SET_ENC_NO_MITM(&attr_md.read_perm);
>     BLE_GAP_CONN_SEC_MODE_SET_ENC_NO_MITM(&attr_md.write_perm);