Letting them live a keeping the boats floating was probably the last option in Israel's list.
What are the proper rules? (rather than it being anything Israel says it is) Diversion is only allowed if there is a danger to a search art sea (which would not be the case for a few boxes of Medical supplies) and it needs the permission of the ships Captain. Barring those conditions diversion is an illegal act. (so was keeping the ships and passengers in the first floatilla)
San Remo Manual on International Law Applicable to Armed Conflicts at Sea, 12 June 1994
SECTION III : ENEMY VESSELS AND AIRCRAFT EXEMPT FROM ATTACK
Classes of vessels exempt from attack
47. The following classes of enemy vessels are exempt from attack:
(a) hospital ships;
(b) small craft used for coastal rescue operations and other medical transports;
(c) vessels granted safe conduct by agreement between the belligerent parties including:
(i) cartel vessels, e.g., vessels designated for and engaged in the transport of prisoners of war;
(ii) vessels engaged in humanitarian missions, including vessels carrying supplies indispensable to the survival of the civilian population, and vessels engaged in relief actions and rescue operations;
(d) vessels engaged in transporting cultural property under special protection;
(e) passenger vessels when engaged only in carrying civilian passengers;
(f) vessels charged with religious, non-military scientifc or philanthropic missions, vessels collecting scientific data of likely military applications are not protected;
(g) small coastal fishing vessels and small boats engaged in local coastal trade, but they are subject to the regulations of a belligerent naval commander operating in the area and to inspection;
(h) vessels designated or adapted exclusively for responding to pollution incidents in the marine environment;
(i) vessels which have surrendered;
(j) life rafts and life boats.
Conditions of exemption
48. Vessels listed in paragraph 47 are exempt from attack only if they:
(a) are innocently employed in their normal role;
(b) submit to identification and inspection when required; and
(c) do not intentionally hamper the movement of combatants and obey orders to stop or move out of the way when required.
SECTION II : VISIT AND SEARCH OF MERCHANT VESSELS
Basic rules
118. In exercising their legal rights in an international armed conflict at sea, belligerent warships and military aircraft have a right to visit and search merchant vessels outside neutral waters where there are reasonable grounds for suspecting that they are subject to capture.
119. As an alternative to visit and search, a neutral merchant vessel may, with its consent, be diverted from its declared destination.
Merchant vessels under convoy of accompanying neutral warships
120. A neutral merchant vessel is exempt from the exercise of the right of visit and search if it meets the following conditions:
(a) it is bound for a neutral port;
(b) it is under the convoy of an accompanying neutral warship of the same nationality or a neutral warship of a State with which the flag State of the merchant vessel has concluded an agreement providing for such convoy;
(c) the flag State of the neutral warship warrants that the neutral merchant vessel is not carrying contraband or otherwise engaged in activities inconsistent with its neutral status; and
(d) the commander of the neutral warship provides, if requested by the commander of an intercepting belligerent warship or military aircraft, all information as to the character of the merchant vessel and its cargo as could otherwise be obtained by visit and search.
Diversion for the purpose of visit and search
121. If visit and search at sea is impossible or unsafe, a belligerent warship or military aircraft may divert a merchant vessel to an appropriate area or port in order to exercise the right of visit and search.
Measures of supervision
122. In order to avoid the necessity of visit and search, belligerent States may establish reasonable measures for the inspection of cargo of neutral merchant vessels and certification that a vessel is not carrying contraband.
123. The fact that a neutral merchant vessel has submitted to such measures of supervision as the inspection of its cargo and grant of certificates of non-contraband cargo by one belligerent is not an act of unneutral service with regard to an opposing belligerent.
124. In order to obviate the necessity for visit and search, neutral States are encouraged to enforce reasonable control measures and certification procedures to ensure that their merchant vessels are not carrying contraband.