I just wanted to echo what Nicolai said and add my, potentially unnecessary, take.
I think you've run head first into the world of inconsistent wordings on cards and for rules. For a while, I believe there was a mantra of "If it isn't there, it isn't there." In this case, when I read the card text I see no mention of the attack replacing any automatic attack your company may face by deciding to enter their new site (as you mentioned, during the site phase) and infer then that this is an additional attack the company must face. It lacks specific language we see on other cards that would look like, in one example: "this attack cancels the normal automatic attacks at the company's new site". Note that there is a clarification that "Otherwise" should be read as "Alternatively".
While I'm not certain of the technical soundness of the following, here's another way I'd look at it:
When this card is played, at the end of the Org Phase, the new site card is in play, but face down. The Automatic Attack on the new site card is not in play and therefore cannot be targeted for removal - or for exchange. The exception being, obviously, a company that doesn't move and their new site is their current site. Compare to the card Stealth:
Scout only. Tap a scout to play at the end of the organization phase only if the scout's company size is less than three. No creature hazards may be played on his company this turn.
This card does prevent creatures from attacking the company in a future phase (i.e. it's played in the Org Phase but prevents the play of cards that would lead to an attack during the Movement/ Hazard Phase). However, it does not specifically target a creature hazard card and cancel the attack, it simply states that no creature hazards may be played. Ash Mountains lacks any mention that Automatic Attacks cannot be levied against a company - which would be particularly difficult since the Automatic Attacks are written directly on the new site card and their being in play are indelibly linked with the play of the new site.
A quick additional comparison with a card that does eliminate the Automatic Attack, Rebuild the Town (errata included):
Playable during the site phase on a non-Dragon's lair, non-Under-deeps Ruins & Lairs. The site becomes a Border-hold and loses all automatic-attacks. Discard Rebuild the Town when the site is discarded or returned to its location deck.
Here you have the card being played during the site phase, at a point when the site (and Automatic Attack) are clearly in play.
There are a number of other general resources you can turn to, some include:
(a) These forums are searchable (obvious).
(b) There is a Combined Rulings File (CRF) along with errata available currently here:
http://www.meccg.net/netherlands/meccg/ ... rules.html
(c) There are CoE and NetRep ruling digests that were released after the CRF and are collected (individually) online and also available currently at the link above in (b). I would bet some have gone through these files and compiled a single, searchable document. Bandobras Took has under"took" an endeavor to combine these files, along with his and some others' commentary. He's generously made progressing versions available under a sticky topic labeled Universal Rules Document in this forum; Nicolai has provided the link to the topic above. In general, the digests seem to focus more on card-specific interpretations and in some cases debated game mechanics.
(d) Card of the Day & Play and Examples file are unofficial documents but can be another viewpoint and interesting background. Some Card of the Day topics are on this forum and I found some archives here:
http://trevorstone.org/metw/cotd/. The Play and Examples file has card-specific notes and is located here:
http://www.meccg.net/dforum/viewtopic.php?t=2076
If any of these resources should fall short, please keep asking questions. There are no insignificant questions - the community still struggles with the legacy of a visionary game that has held up to an impossible lifetime of play and scrutiny.