The temporal attack on Voyager was held off briefly by Voyager's temporal shielding, during which time Voyager was able to escape. That means that the temporal incursion was unsuccessful and no time change occured, so once Voyager was out of range (i.e., was too far away for the Kyana Prime to fire on them a second time) they could safely drop the temporal shielding. It was not necessary for Voyager and its crew to remain temporally shielded indefinitely as you suggest.
Of course, it is true that any individual escape pods that had the bad fortune to encounter the Kyana Prime would be vulnerable to attack from the temporal weapon - but for that matter they would also be extremely vulnerable to conventional weaponry. They had at least a fighting chance of sneaking out of Krenim space undetected, and Captain Janeway had little choice in the matter, since Voyager was no longer capable of supporting the full crew:
"Voyager can no longer sustain its crew. I promised myself that I would never give this order, that I would never break up this family --- but asking you to stay would be asking you to die."
(If in doubt, we can see that leaving the ship did not put the crew in immediate danger on-screen in the final scene from Year of Hell, Part 1, which shows the escape pods safely departing Voyager. In fact, in order to allow the escape pods to leave Voyager must have first had to drop its shields, so had the temporal incursion been successful Voyager would have already ceased to exist by that point!)