So. to address thread topic (and premise presented in OP), let's reiterate.
1) What is known:
- The residents of the municipality of Bondi Beach (Sydney) opposed the construction of a synagogue on grounds of such a building, specifically in view of the religion it represents, constituting a security risk in that attacks on visitors (possibly extending to others in the vicinity) could be expected.
- The council has followed the line of argument and denied permission, with a court subsequently confirming (and upholding) that decision. Question being, has it really, when surmising the last point raised here towards the end?
2) What is also known (and has been presented here):
- There exists within parts of Australian society an undercurrent of anti-semitism that has led to abuse of Jews, attacks upon them and has shown to be on the rise (of incidents occurring) in 2016. This has also led to synagogues being attacked, albeit in the "mere" material manner of being smeared with anti-semitic slogans, graffiti etc. but that takes nothing away from physical attacks upon Jews having happened altogether.
- The concerns voiced by residents over security risks addressed potential attacks in general, specific concerns of (equally specific) attacks by jihadists were neither part of the council's objection nor of the court ruling (in its favour).
3) What is equally known but takes the whole issue to levels of ridiculousness where the council's arguments (and subsequently those of the court) are concerned:
- Both council and court used the proposed design as evidence of the construction posing a security risk, yet (Catch-22)...............
- the council also said if the design was changed to boost security (presumably so lessening the risk) this would be unacceptable because it would be too unsightly for the neighborhood.
4) What one may speculate upon (such speculations taking the place of knowledge as little as the original premise here:
- does the security risk seen by the residents of Bondi beach reside in their knowledge of Jews being "unpopular" with many Australians (whatever their number may be), this condition then leading to the assumption of future attacks?
- Is anti-semitism shared into in Bondi beach and if so, by how many, on the pretext of "we don't want a synagogue here, it's not representative of the nature of our neighborhood"?
- Why, (if we follow the premise of jihadims posing the greatest threat to "other" houses of worship) did no such concerns arise (from "unsightly" to "could incur attacks") over (just one) new Christian church opening next month in greater Sydney? Considering that IS has repeatedly declared war not just on "the West" but on Christianity in general? Putting that declaration of war into action by attacking Christians and their houses of worship all over the M.E. and in one instance so far (thankfully, in it as yet having been only one) in France?
- do equal concerns by the same council extend to the Central synagogue at Bondi junction, nor far from the location described here and serviced by the very council?
- Indeed, seeing how the opinion piece that the OP links to states the council as being primarily responsible for refusing building permission, what is one to make of this?
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A technical planning decision (at least as far as the general manager of Waverley Council sees it as being) constitutes caving in to Islamic terrorism?
Does anyone else see that reasons are manifold and the exclusive one given in the premise initially presented by this thread can hardly be seen as logically conclusive?