There is plenty of time travel and bending of space time throughout the entire series all the way back to HL1 and the expansions.
Tons of hints of the G-Man's interest in Alyx in Episode 2.
What they did here was perfect and fits in extremely well with everything setup in the series so far.
I've been playing the series since day dot and I completely disagree. Time travel in Half-Life has generally followed a concrete rule of forward momentum. There has not been, to my knowledge, any timeline inconsistencies, paradoxes, change-the-past, multiple timelines/events, etc suggested in the narrative across the entire game. At the very least in the core canon, which is Half-Life, Half-Life 2, Episode 1, Episode 2, Portal, and Portal 2.
Causality has been a major factor in all the games, and all time travel and dimensional shifting has been limited by the subjective perception of time, not the altering of time. Forward time dilation has occurred, but again only by considering causality and the importance of the past being unchangeable. The implications have instead be that while the G-Man seems to break numerous laws of physics, including time, his application of influence has been limited entirely to causality within a single timeline, such as putting a person in stasis and returning them when most convenient. Teleportation is the same. Combine and Resistance technology follows specific rules (including the time dilation of slow teleport), dimensional crossing does not send a person backwards in time, and both the G-Man and Vorts appear bound to a general linearity and causality in the passage of time even if they are able to stall it.
Having Alyx essentially pulled into the future is not a break of these rules. It's on par with Gordon's stasis. Alyx changing the future and completely retconning the final events of Episode 2 is unheard of in the series and introduces numerous narrative problems. How many Alyx's are there? How did these events changing influence the perception of those witnessing them? Can the past be changed so readily? Does it create multiple timelines, or is it still linear? If it's linear, why did the events happen at all instead of being circular and non-contradictory? And if there are multiple timelines what timeline are we now in, and does it even really matter? Is there a timeline with dead Eli? To what limit do characters like G-Man have to directly changing the course of events that have already happened, not just influencing events that haven't happened yet?
It's poor form, as far as I'm concerned. It's pointless and complicated for no reason, and muddiness a lot of the rawer, causality based science fiction that Half-Life is known for. I've got no problem with time dilation. I've got no problem with goofy G-Man premonitions and manipulation of events over a long period of time. But changing the future that we've already experience, via time travel, for a retcon? Complicating the narrative with questions of multiple timelines due to the inherent paradoxal inconsistencies of it all now? Rubbish writing and completely unnecessary.